Help text (-h) for all tools¶
sct_analyze_lesion¶
--
Spinal Cord Toolbox (7.0)
sct_analyze_lesion -h
--
usage: sct_analyze_lesion -m <file> [-s <file>] [-i <file>] [-f <str>]
[-perslice <int>] [-ofolder <folder>] [-qc <folder>]
[-qc-dataset <str>] [-qc-subject <str>] [-h]
[-v <int>] [-profile-time [<file>]]
[-trace-memory [<folder>]] [-r {0,1}]
Compute statistics on segmented lesions. The function assigns an ID value to
each lesion (1, 2, 3, etc.) and then outputs morphometric measures for each
lesion:
- volume `[mm^3]`: volume of the lesion
- length `[mm]`: maximal length along the Superior-Inferior (SI) axis across
all sagittal slices of the lesion
- width `[mm]`: maximal width along the Anterior-Posterior (AP) axis across
all sagittal slices of the lesion
- max_equivalent_diameter `[mm]`: maximum diameter of the lesion, when
approximating the lesion as a circle in the axial plane
- max_axial_damage_ratio `[]`: maximum ratio of the lesion area divided by the
spinal cord area
- interpolated_midsagittal_slice: number (float) corresponding to the
interpolated midsagittal slice
- length_interpolated_midsagittal_slice `[mm]`: length of the lesion along the
Superior-Inferior (SI) axis in the **interpolated midsagittal slice**
- width_interpolated_midsagittal_slice `[mm]`: width of the lesion along the
Anterior-Posterior (AP) axis the **interpolated midsagittal slice**
- interpolated_dorsal_bridge_width `[mm]`: width of spared tissue dorsal to
the spinal cord lesion in the **interpolated midsagittal slice**
- interpolated_ventral_bridge_width `[mm]`: width of spared tissue ventral to
the spinal cord lesion in the **interpolated midsagittal slice**
- dorsal_bridge_width `[mm]`: width of spared tissue dorsal to the spinal cord
lesion (i.e. towards the posterior direction of the AP axis) for each
sagittal slice containing the lesion
- ventral_bridge_width `[mm]`: width of spared tissue ventral to the spinal
cord lesion (i.e. towards the anterior direction of the AP axis) for each
sagittal slice containing the lesion
If the proportion of lesion in each region (e.g. WM and GM) does not sum up to
100%, it means that the registered template does not fully cover the lesion. In
that case you might want to check the registration results.
MANDATORY ARGUMENTS:
-m <file> Binary mask of lesions (lesions are labeled as "1").
OPTIONAL ARGUMENTS:
-s <file> Spinal cord centerline or segmentation file, which will
be used to correct morphometric measures with cord angle
with respect to slice. (e.g. `t2_seg.nii.gz`)
If provided, then the lesion volume, length, diameter,
axial damage ratio, and tissue bridges will be computed.
Otherwise, if not provided, then only the lesion volume
will be computed.
-i <file> Image from which to extract average values within
lesions (e.g. "t2.nii.gz"). If provided, the function
computes the mean and standard deviation values of this
image within each lesion.
-f <str> Path to folder containing the atlas/template registered
to the anatomical image. If provided, the function
computes:
1. for each lesion, the proportion of that lesion
within each vertebral level and each region of the
template (e.g. GM, WM, WM tracts). Each cell contains
a percentage value representing how much of the lesion
volume exists within the region indicated by the
row/column (rows represent vertebral levels, columns
represent ROIs). The percentage values are summed to
totals in both the bottom row and the right column,
and the sum of all cells is 100 (i.e. 100 percent of
the lesion), found in the bottom-right.
2. the proportions of each ROI (e.g. vertebral level,
GM, WM) occupied by lesions.
These percentage values are stored in different pages of
the output `lesion_analysis.xlsx` spreadsheet; one page
for each lesion (a.) plus a final page summarizing the
total ROI occupation of all lesions (b.)
-perslice <int> Specify whether to aggregate atlas metrics (`-f` option)
per slice (`-perslice 1`) or per vertebral level
(default behavior). (default: 0)
-ofolder <folder> Output folder (e.g. "."). Default is the current folder
("."). (default: .)
-qc <folder> The path where the quality control generated content
will be saved.
-qc-dataset <str> If provided, this string will be mentioned in the QC
report as the dataset the process was run on.
-qc-subject <str> If provided, this string will be mentioned in the QC
report as the subject the process was run on.
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_analyze_texture¶
--
Spinal Cord Toolbox (7.0)
sct_analyze_texture -h
--
usage: sct_analyze_texture -i <file> -m <file> [-feature <str>]
[-distance <int>] [-angle <list>] [-dim {ax,sag,cor}]
[-ofolder <folder>] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
[-r {0,1}]
Extraction of gray level co-occurence matrix (GLCM) texture features from an
image within a given mask. The textures features are those defined in the sckit-
image implementation: https://scikit-
image.org/docs/dev/api/skimage.feature.html#graycoprops. This function outputs
one nifti file per texture metric
(contrast,dissimilarity,homogeneity,energy,correlation,ASM) and per orientation
called fnameInput_feature_distance_angle.nii.gz. Also, a file averaging each
metric across the angles, called fnameInput_feature_distance_mean.nii.gz, is
output.
MANDATORY ARGUMENTS:
-i <file> Image to analyze. Example: `t2.nii.gz`
-m <file> Image mask. Example: `t2_seg.nii.gz`
OPTIONAL ARGUMENTS:
-feature <str> List of GLCM texture features (separate arguments with
`,`). (default: contrast,dissimilarity,homogeneity,energ
y,correlation,ASM)
-distance <int> Distance offset for GLCM computation, in pixel
(suggested distance values between 1 and 5). (default:
1)
-angle <list> List of angles for GLCM computation, separate arguments
with `,`, in degrees (suggested distance values between
0 and 179). (default: 0,45,90,135)
-dim {ax,sag,cor} Compute the texture on the axial (ax), sagittal (sag) or
coronal (cor) slices. (default: ax)
-ofolder <folder> Output folder. (default: ./texture)
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_apply_transfo¶
--
Spinal Cord Toolbox (7.0)
sct_apply_transfo -h
--
usage: sct_apply_transfo -i <file> -d <file> -w <file> [<file> ...]
[-winv <file> [<file> ...]] [-crop {0,1,2}] [-o <file>]
[-x {nn,linear,spline,label}] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
[-r {0,1}]
Apply transformations. This function is a wrapper for antsApplyTransforms
(ANTs).
MANDATORY ARGUMENTS:
-i <file> Input image. Example: `t2.nii.gz`
-d <file> Destination image. For warping input images, the
destination image defines the spacing, origin, size, and
direction of the output warped image. Example:
`dest.nii.gz`
-w <file> [<file> ...]
Transformation(s), which can be warping fields (nifti
image) or affine transformation matrix (text file).
Separate with space. Example: `warp1.nii.gz
warp2.nii.gz`
OPTIONAL ARGUMENTS:
-winv <file> [<file> ...]
Affine transformation(s) listed in flag -w which should
be inverted before being used. Note that this only
concerns affine transformation (not warping fields). If
you would like to use an inverse warping field, then
directly input the inverse warping field in flag -w.
-crop {0,1,2} Crop Reference. 0: no reference, 1: sets background to
0, 2: use normal background. (default: 0)
-o <file> Filename to use for the output image (i.e. the
transformed image). Example: `out.nii.gz`
-x {nn,linear,spline,label}
Interpolation method.
Note: The `label` method is a special interpolation
method designed for single-voxel labels (e.g. disc
labels used as registration landmarks, compression
labels, etc.). This method is necessary because
classical interpolation may corrupt the values of
single-voxel labels, or cause them to disappear
entirely. The function works by dilating each label,
applying the transformation using nearest neighbour
interpolation, then extracting the center-of-mass of
each transformed 'blob' to get a single-voxel output
label. Because the output is a single-voxel label, the
`-x label` method is not appropriate for multi-voxel
labeled segmentations (such as spinal cord or lesion
masks).
(default: spline)
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_compute_ernst_angle¶
--
Spinal Cord Toolbox (7.0)
sct_compute_ernst_angle -h
--
usage: sct_compute_ernst_angle -tr <float> [-t1 <float>] [-b <float> <float>]
[-o <str>] [-ofig <str>] [-h] [-v <int>]
[-profile-time [<file>]]
[-trace-memory [<folder>]]
Function to compute the Ernst Angle.
For examples of T1 values in the brain, see Wansapura et al. NMR relaxation
times in the human brain at 3.0 tesla. Journal of magnetic resonance imaging :
JMRI (1999) vol. 9 (4) pp. 531-8. T1 in WM: 832msT1 in GM: 1331ms
MANDATORY ARGUMENTS:
-tr <float> Value of TR (in ms) to get the Ernst Angle. Example:
`2000`
OPTIONAL ARGUMENTS:
-t1 <float> T1 value (in ms). (default: 832.0)
-b <float> <float> Min/Max range of TR (in ms) separated with space. Only
use with `-v 2`. (default: [500, 3500])
-o <str> Name of the output file containing Ernst angle result.
(default: ernst_angle.txt)
-ofig <str> Name of the output graph. Only use with `-v 2`.
(default: ernst_angle.png)
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_compute_hausdorff_distance¶
--
Spinal Cord Toolbox (7.0)
sct_compute_hausdorff_distance -h
--
usage: sct_compute_hausdorff_distance -i <file> [-d <file>] [-thinning {0,1}]
[-resampling <float>] [-o <str>] [-h]
[-v <int>] [-profile-time [<file>]]
[-trace-memory [<folder>]]
Compute the Hausdorff's distance between two binary images which can be thinned
(ie skeletonized). If only one image is inputted, it will be only thinned
MANDATORY ARGUMENTS:
-i <file> First image on which you want to find the skeleton.
Example: `t2star_manual_gmseg.nii.gz`
OPTIONAL ARGUMENTS:
-d <file> Second Image on which you want to find the skeleton.
Example: `t2star_manual_gmseg.nii.gz`
-thinning {0,1} Thinning : find the skeleton of the binary images using
the Zhang-Suen algorithm (1984) and use it to compute
the hausdorff's distance (default: 1)
-resampling <float> Pixel size in mm to resample to. (default: 0.1)
-o <str> Name of the output file. (default:
hausdorff_distance.txt)
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_compute_compression¶
--
Spinal Cord Toolbox (7.0)
sct_compute_compression -h
--
usage: sct_compute_compression -i <file> -vertfile <file> -l <file>
[-extent <float>] [-distance <float>] [-o <file>]
[-normalize-hc <int>]
[-metric {diameter_AP,area,diameter_RL,eccentricity,solidity}]
[-sex {F,M}] [-age [0 100] [0 100]] [-h]
[-v <int>] [-profile-time [<file>]]
[-trace-memory [<folder>]]
Compute normalized morphometric metrics to assess:
- spinal cord compression using MSCC (maximum spinal cord compression)
- spinal canal stenosis using MCC (maximum canal compromise)
Metrics are normalized using the non-compressed levels above and below the
compression site using the following equation:
```
ratio = (1 - mi/((ma+mb)/2))
```
Where mi: metric at the compression level, ma: metric above the compression
level, mb: metric below the compression level.
Additionally, if the `-normalize-hc` flag is used, metrics are normalized using
a database built from healthy control subjects. This database uses the PAM50
template as an anatomical reference system.
References:
- Sandrine Bédard, Jan Valošek, Maryam Seif, Armin Curt, Simon Schading,
Nikolai Pfender, Patrick Freund, Markus Hupp, Julien Cohen-Adad. Normalizing
Spinal Cord Compression Morphometric Measures: Application in Degenerative
Cervical Myelopathy. medRxiv 2024.03.13.24304177
https://doi.org/10.1101/2024.03.13.24304177
- Miyanji F, Furlan JC, Aarabi B, Arnold PM, Fehlings MG. Acute cervical
traumatic spinal cord injury: MR imaging findings correlated with neurologic
outcome--prospective study with 100 consecutive patients. Radiology
2007;243[3]:820-827.
https://doi.org/10.1148/radiol.2433060583
- `-normalize-hc` flag:
Valošek J, Bédard S, Keřkovský M, Rohan T, Cohen-Adad J. A database of the
healthy human spinal cord morphometry in the PAM50 template space. Imaging
Neuroscience 2024; 2 1–15.
https://doi.org/10.1162/imag_a_00075
MANDATORY ARGUMENTS:
-i <file> Spinal cord or spinal canal segmentation mask to compute
morphometrics from. If spinal cord segmentation is
provided, MSCC is computed. If spinal canal segmentation
(spinal cord + CSF) is provided, MCC is computed.
Example: `sub-001_T2w_seg.nii.gz`
Note: If no normalization is wanted (i.e., if the
`-normalize-hc` flag is not specified), metric ratio
will take the average along the segmentation centerline.
-vertfile <file> Vertebral labeling file. Example:
`sub-001_T2w_seg_labeled.nii.gz`
Note: The input and the vertebral labelling file must be
in the same voxel coordinate system and must match the
dimensions between each other.
-l <file> NIfTI file that includes labels at the compression
sites. Each compression site is denoted by a single
voxel of value `1`. Example:
`sub-001_T2w_compression_labels.nii.gz`
Note: The input and the compression label file must be
in the same voxel coordinate system and must match the
dimensions between each other.
OPTIONAL ARGUMENTS:
-extent <float> Extent (in mm) to average metrics of healthy levels in
superior-inferior direction. (default: 20.0)
-distance <float> Distance (in mm) in the superior-inferior direction from
the compression to average healthy slices. (default:
10.0)
-o <file> Output CSV file name. If not provided, the suffix
`_compression_metrics` is added to the file name
provided by the flag `-i`.
NORMALIZATION ARGUMENTS:
-normalize-hc <int> Set to 1 to normalize the metrics using a database of
healthy controls. Default: 0.
Note: This flag should not be set to 1 when computing
the MCC (i.e. using spinal canal segmentation),
and should only be used when computing the MSCC (i.e.
using spinal cord segmentation).
-metric {diameter_AP,area,diameter_RL,eccentricity,solidity}
Metric to normalize. (default: diameter_AP)
-sex {F,M} Sex of healthy subject to use for the normalization. By
default, both sexes are used.
-age [0 100] [0 100] Age range of healthy subjects to use for the
normalization. Example: `-age 60 80`. By default, all
ages are considered.
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_compute_mtr¶
--
Spinal Cord Toolbox (7.0)
sct_compute_mtr -h
--
usage: sct_compute_mtr -mt0 <float> -mt1 <float> [-thr THR] [-o <str>] [-h]
[-v <int>] [-profile-time [<file>]]
[-trace-memory [<folder>]]
Compute magnetization transfer ratio (MTR). Output is given in percentage.
MANDATORY ARGUMENTS:
-mt0 <float> Image without MT pulse (MT0)
-mt1 <float> Image with MT pulse (MT1)
OPTIONAL ARGUMENTS:
-thr THR Threshold to clip MTR output values in case of division
by small number. This implies that the output image
range will be [-thr, +thr]. Default: `100`. (default:
100)
-o <str> Path to output file. (default: ./mtr.nii.gz)
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_compute_mtsat¶
--
Spinal Cord Toolbox (7.0)
sct_compute_mtsat -h
--
usage: sct_compute_mtsat -mt <file> -pd <file> -t1 <file> [-trmt <float>]
[-trpd <float>] [-trt1 <float>] [-famt <float>]
[-fapd <float>] [-fat1 <float>] [-b1map <file>]
[-omtsat <str>] [-ot1map <str>] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
Compute MTsat and T1map. Reference: Helms G, Dathe H, Kallenberg K, Dechent P.
High-resolution maps of magnetization transfer with inherent correction for RF
inhomogeneity and T1 relaxation obtained from 3D FLASH MRI. Magn Reson Med
2008;60(6):1396-1407.
MANDATORY ARGUMENTS:
-mt <file> Image with MT_ON
-pd <file> Image PD weighted (typically, the MT_OFF)
-t1 <file> Image T1-weighted
JSON SIDECAR OVERRIDES:
Any arguments within this group will override their corresponding values in
the JSON side-car files of the MRI sequences you have provided. Otherwise, all
values will be fetched from the associated JSON sidecar, assuming it exists.
If not, you should provide the corresponding metrics using these arguments.
-trmt <float> TR [in s] for the MT image (MT on).
-trpd <float> TR [in s] for proton density weighted image (MT off).
-trt1 <float> TR [in s] for the T1-weighted image.
-famt <float> Flip angle [in deg] for the MT-weighted image.
-fapd <float> Flip angle [in deg] for the PD-weighted image.
-fat1 <float> Flip angle [in deg] for the T1-weighted image.
OPTIONAL ARGUMENTS:
-b1map <file> B1 map
-omtsat <str> Output file for MTsat (default: mtsat.nii.gz)
-ot1map <str> Output file for T1map (default: t1map.nii.gz)
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_compute_snr¶
--
Spinal Cord Toolbox (7.0)
sct_compute_snr -h
--
usage: sct_compute_snr -i <file> [-m <file>] [-method {diff,mult,single}]
[-m-noise <file>] [-vol <str>] [-rayleigh {0,1}]
[-o <str>] [-h] [-v <int>] [-profile-time [<file>]]
[-trace-memory [<folder>]] [-r {0,1}]
Compute SNR using methods described in [Dietrich et al., Measurement of signal-
to-noise ratios in MR images: Influence of multichannel coils, parallel imaging,
and reconstruction filters. J Magn Reson Imaging 2007; 26(2): 375-385].
MANDATORY ARGUMENTS:
-i <file> Image to compute the SNR on. Example: `b0s.nii.gz`
- For `-method diff` and `-method mult`, the image
must be 4D, as SNR will be computed along the 4th
dimension.
- For `-method single`, the image can either be 3D or
4D. If a 4D image is passed, a specific 3D volume
should be specified using the `-vol` argument.
OPTIONAL ARGUMENTS:
-m <file> Binary (or weighted) mask within which SNR will be
averaged. Example: `dwi_moco_mean_seg.nii.gz`
-method {diff,mult,single}
Method to use to compute the SNR:
- `diff`: Substract two volumes (defined by -vol) and
estimate noise variance within the ROI (flag `-m` is
required). Requires a 4D volume.
- `mult`: Estimate noise variance over time across
volumes specified with `-vol`. Requires a 4D volume.
- `single`: Compute the mean signal in the mask
specified by `-m` and estimate the noise variance in a
mask specified by `-m-noise`. If the noise mask is in
the background (air), the noise variance needs to be
corrected for Rayleigh distribution (set `-rayleigh
1`). If the noise mask is located in a region with
high signal (eg: tissue), noise distribution can be
assumed Gaussian and there is no need to correct for
Rayleigh distribution (use `-rayleigh 0`). This
implementation corresponds to the SNRstdv in the
Dietrich et al. article. Uses a 3D or a 4D volume. If
a 4D volume is input, the volume to compute SNR on is
specified by `-vol`. (default: diff)
-m-noise <file> Binary (or weighted) mask within which noise will be
calculated. Only valid for `-method single`.
-vol <str> Volumes to compute SNR from. Separate with `,` (Example:
`-vol 0,1`), or select range using `:` (Example: `-vol
2:50`).
If this argument is not passed:
- For `-method mult`, all volumes will be used.
- For `-method diff`, the first two volumes will be
used.
- For `-method single`, the first volume will be used.
-rayleigh {0,1} Correct for Rayleigh distribution. It is recommended to
always use this correction for the 'diff' method and to
use it with the 'single' method in case the noise mask
is taken in a region with low SNR (e.g., the air).
(default: 1)
-o <str> File name to write the computed SNR to.
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_convert¶
--
Spinal Cord Toolbox (7.0)
sct_convert -h
--
usage: sct_convert -i <file> -o <str> [-squeeze {0,1}] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
Convert image file to another type.
MANDATORY ARGUMENTS:
-i <file> File input. Example: `data.nii.gz`
-o <str> File output (including the file's extension). Example:
`data.nii`
OPTIONAL ARGUMENTS:
-squeeze {0,1} Squeeze data dimension (remove unused dimension)
(default: 1)
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_create_mask¶
--
Spinal Cord Toolbox (7.0)
sct_create_mask -h
--
usage: sct_create_mask -i <file> -p <str> [-size <str>]
[-f {cylinder,box,gaussian}] [-o <str>] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
[-r {0,1}]
Create mask along z direction.
MANDATORY ARGUMENTS:
-i <file> Image to create mask on. Only used to get header. Must
be 3D. Example: `data.nii.gz`
-p <str> Process to generate mask.
- `coord,XxY`: Center mask at the X,Y coordinates.
Example: `coord,20x15`
- `point,FILE`: Center mask at the X,Y coordinates of
the label defined in input volume FILE. Example:
`point,label.nii.gz`
- `center`: Center mask in the middle of the FOV
`[nx/2, ny/2]`.
- `centerline,FILE`: At each slice, the mask is
centered at the spinal cord centerline, defined by the
input segmentation FILE. Example:
`centerline,t2_seg.nii.gz`
(default: center)
OPTIONAL ARGUMENTS:
-size <str> Diameter of the mask in the axial plane, given in pixel
(Example: `35`) or in millimeter (Example: `35mm`). If
shape=gaussian, size instead corresponds to "sigma"
(Example: `45`). (default: 41)
-f {cylinder,box,gaussian}
Shape of the mask (default: cylinder)
-o <str> Name of output mask, Example: `data.nii.gz`
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_crop_image¶
--
Spinal Cord Toolbox (7.0)
sct_crop_image -h
--
usage: sct_crop_image -i <file> [-o <str>] [-dilate <list>] [-g {0,1}]
[-m <file>] [-ref <file>] [-xmin <int>] [-xmax <int>]
[-ymin <int>] [-ymax <int>] [-zmin <int>] [-zmax <int>]
[-b <int>] [-h] [-v <int>] [-profile-time [<file>]]
[-trace-memory [<folder>]]
Tools to crop an image. Either via command line or via a Graphical User
Interface (GUI). See example usage at the end.
MANDATORY ARGUMENTS:
-i <file> Input image. Example: `t2.nii.gz`
OPTIONAL ARGUMENTS:
-o <str> Output image. By default, the suffix '_crop' will be
added to the input image.
-dilate <list> Number of extra voxels to keep around the bounding box
on each side. Can be specified as a single number, or a
list of 3 numbers separated by `x`. For example:
- `-dilate 5` will add a margin of 5 voxels in each
direction
- `-dilate 2x3x0` will add margin of 2 voxels on each
side in the x-axis, 3 voxels on each side in the
y-axis, and no extra margin in the z-axis.
-g {0,1} `0`: Cropping via command line | `1`: Cropping via GUI.
Has priority over `-m`. (default: 0)
-m <file> Binary mask that will be used to extract bounding box
for cropping the image. Has priority over `-ref`.
-ref <file> Image which dimensions (in the physical coordinate
system) will be used as a reference to crop the input
image. Only works for 3D images. Has priority over
min/max method.
-xmin <int> Lower bound for cropping along X. (default: 0)
-xmax <int> Higher bound for cropping along X. Setting `-1` will
crop to the maximum dimension (i.e. no change), `-2`
will crop to the maximum dimension minus 1 slice, etc.
(default: -1)
-ymin <int> Lower bound for cropping along Y. (default: 0)
-ymax <int> Higher bound for cropping along Y. Follows the same
rules as xmax. (default: -1)
-zmin <int> Lower bound for cropping along Z. (default: 0)
-zmax <int> Higher bound for cropping along Z. Follows the same
rules as xmax. (default: -1)
-b <int> If this flag is declared, the image will not be cropped
(i.e. the dimension will not change). Instead, voxels
outside the bounding box will be set to the value
specified by this flag. For example, to have zeros
outside the bounding box, use: '-b 0'
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
EXAMPLES:
- To crop an image using the GUI (this does not allow to crop along the right-
left dimension):
```
sct_crop_image -i t2.nii.gz -g 1
```
- To crop an image using a binary mask:
```
sct_crop_image -i t2.nii.gz -m mask.nii.gz
```
- To crop an image using a reference image:
```
sct_crop_image -i t2.nii.gz -ref mt1.nii.gz
```
- To crop an image by specifying min/max (you don't need to specify all
dimensions). In the example below, cropping will occur between x=5 and x=60, and
between z=5 and z=zmax-1
```
sct_crop_image -i t2.nii.gz -xmin 5 -xmax 60 -zmin 5 -zmax -2
```
- To crop an image using a binary mask, and keep a margin of 5 voxels on each
side in the x and y directions only:
```
sct_crop_image -i t2.nii.gz -m mask.nii.gz -dilate 5x5x0
```
sct_deepseg¶
--
Spinal Cord Toolbox (7.0)
sct_deepseg -h
--
usage: sct_deepseg TASK ...
Examples:
sct_deepseg spinalcord -h
sct_deepseg gm_mouse_t1 -install
sct_deepseg lesion_ms -i cMRI3712.nii.gz
View available tasks:
sct_deepseg -h
sct_deepseg -task-details
Segment an anatomical structure or pathologies according to the specified deep
learning model.
positional arguments:
TASK Segmentation task to perform.
- To install a task, run `sct_deepseg TASK -install`
- To segment an image, run `sct_deepseg TASK -i
input.nii.gz`
- To view additional options for a given task, run
`sct_deepseg TASK -h`
OPTIONAL ARGUMENTS:
-task-details Display a list of tasks, along with detailed descriptions
(including information on how the model was trained, what data
it was trained on, and any performance evaluations, associated
papers, etc. it may have)
-h, --help Show this help message and exit.
TASK DESCRIPTION
================================================================================
SPINAL CORD
--------------------------------------------------------------------------------
[91mspinalcord [0m[91mSpinal cord segmentation agnostic to MRI contrasts[0m
[91msc_epi [0m[91mSpinal cord segmentation for EPI-BOLD fMRI data[0m
[91msc_lumbar_t2 [0m[91mLumbar cord segmentation with 3D UNet[0m
[91msc_mouse_t1 [0m[91mCord segmentation on mouse MRI[0m
GRAY MATTER
--------------------------------------------------------------------------------
[91mgm_sc_7t_t2star [0m[91mSC/GM seg on T2*-weighted contrast at 7T[0m
[91mgm_wm_exvivo_t2 [0m[91mGrey/white matter seg on exvivo human T2w[0m
[91mgm_mouse_t1 [0m[91mGray matter segmentation on mouse MRI[0m
[91mgm_wm_mouse_t1 [0m[91mExvivo mouse GM/WM segmentation for T1w contrast[0m
PATHOLOGY
--------------------------------------------------------------------------------
[91mlesion_ms [0m[91mMS lesion segmentation on spinal cord MRI images[0m
[91mlesion_ms_axial_t2 [0m[91mIntramedullary MS lesion and spinal cord segmentation
in Axial T2w MRI[0m
[91mlesion_ms_mp2rage [0m[91mMS lesion segmentation on cropped MP2RAGE data[0m
[91mlesion_sci_t2 [0m[91mIntramedullary SCI lesion and cord segmentation in T2w
MRI[0m
[91mtumor_edema_cavity_t1_t2 [0m[91mMulticlass cord tumor/edema/cavity segmentation[0m
[91mtumor_t2 [0m[91mCord tumor segmentation on T2-weighted contrast[0m
OTHER
--------------------------------------------------------------------------------
[91mgraymatter [0m[91mSegmentation of gray matter agnostic to MRI contrasts
and regions[0m
[91mrootlets_t2 [0m[91mSegmentation of spinal nerve rootlets for T2w
contrast[0m
[91msc_canal_t2 [0m[91mSegmentation of spinal canal on T2w contrast[0m
[91mtotalspineseg [0m[91mIntervertebral discs labeling and vertebrae
segmentation[0m
Legend: [92minstalled[0m | [91mnot installed[0m
To read in-depth descriptions of the training data, model architecture, etc.
used for these tasks, type the following command:
[94m[1msct_deepseg -task-details[0m
sct_deepseg_gm¶
--
Spinal Cord Toolbox (7.0)
sct_deepseg_gm -h
--
usage: sct_deepseg_gm -i <file> [-o <file>] [-m {large,challenge}]
[-thr <float>] [-t] [-qc <str>] [-qc-dataset <str>]
[-qc-subject <str>] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
Spinal Cord Gray Matter (GM) Segmentation using deep dilated convolutions. The
contrast of the input image must be similar to a T2*-weighted image: WM dark, GM
bright and CSF bright. Reference: Perone CS, Calabrese E, Cohen-Adad J. Spinal
cord gray matter segmentation using deep dilated convolutions. Sci Rep
2018;8(1):5966.
MANDATORY ARGUMENTS:
-i <file> Image filename to segment (3D volume). Example:
`t2s.nii.gz`.
OPTIONAL ARGUMENTS:
-o <file> Output segmentation file name. Example:
`sc_gm_seg.nii.gz`
-m {large,challenge} Model to use (large or challenge). The model 'large'
will be slower but will yield better results. The model
'challenge' was built using data from the following
challenge: goo.gl/h4AVar. (default: large)
-thr <float> Threshold to apply in the segmentation predictions, use
0 (zero) to disable it. (default: 0.999)
-t Enable TTA (test-time augmentation). Better results, but
takes more time and provides non-deterministic results.
MISC ARGUMENTS:
-qc <str> The path where the quality control generated content
will be saved.
-qc-dataset <str> If provided, this string will be mentioned in the QC
report as the dataset the process was run on
-qc-subject <str> If provided, this string will be mentioned in the QC
report as the subject the process was run on
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_denoising_onlm¶
--
Spinal Cord Toolbox (7.0)
sct_denoising_onlm -h
--
usage: sct_denoising_onlm -i <file> [-p {Rician,Gaussian}] [-d <int>]
[-std <float>] [-o <str>] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
[-r {0,1}]
Utility function to denoise images. Return the denoised image and also the
difference between the input and the output. The denoising algorithm is based on
the Non-local means methods (Pierrick Coupe, Jose Manjon, Montserrat Robles,
Louis Collins. “Adaptive Multiresolution Non-Local Means Filter for 3D MR Image
Denoising” IET Image Processing, Institution of Engineering and Technology,
2011). The implementation is based on Dipy (https://dipy.org/).
MANDATORY ARGUMENTS:
-i <file> Input NIFTI image to be denoised. Example:
`image_input.nii.gz`
OPTIONAL ARGUMENTS:
-p {Rician,Gaussian} Type of assumed noise distribution. (default: Rician)
-d <int> Threshold value for what to be considered as noise. The
standard deviation of the noise is calculated for values
below this limit. Not relevant if `-std` value is
precised. (default: 80)
-std <float> Standard deviation of the noise. If not specified, it is
calculated using a background of point of values below
the threshold value (parameter `-d`).
-o <str> Name of the output NIFTI image.
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_detect_compression¶
--
Spinal Cord Toolbox (7.0)
sct_detect_compression -h
--
usage: sct_detect_compression -s <file> -discfile <file> [-num-of-slices <int>]
[-angle-corr <int>] [-o <file>] [-h] [-v <int>]
[-profile-time [<file>]]
[-trace-memory [<folder>]]
Predict compression probability in a spinal cord MRI image using spinal cord
shape metrics.
The script process axial slices at the level of intervertebral discs C3/C4
(value: 4) to C6/C7 (value: 7).
Compression categories are determined based on the following cut-offs:
- 'yes' : p > 0.451
- 'possible': 0.345 <= p <= 0.451
- 'no' : p < 0.345
These cut-off values and compression categories were determined by ROC analysis
and the Youden’s index
(the sum of sensitivity and specificity). More info in the reference below.
Reference:
- Horáková M, Horák T, Valošek J, Rohan T, Koriťáková E, Dostál M, Kočica J,
Skutil T, Keřkovský M, Kadaňka Z Jr, Bednařík P, Svátková A, Hluštík P,
Bednařík J. Semi-automated detection of cervical spinal cord compression
with the Spinal Cord Toolbox. Quant Imaging Med Surg 2022; 12:2261–2279.
https://doi.org/10.21037/qims-21-782
MANDATORY ARGUMENTS:
-s <file> Segmentation of the spinal cord, which will be used to
compute the shape metrics. Example: `t2s_seg.nii.gz`.
-discfile <file> File with disc labels. Each label must be a single
voxel. Only label values 4, 5, 6, and 7 (C3/C4 to C6/C7)
are supported for now; all other labels will be ignored.
Labels can be located either at the posterior edge of
the intervertebral discs, or at the orthogonal
projection of each disc onto the spinal cord.
Such a label file can be manually created using:
`sct_label_utils -i IMAGE_REF -create-viewer 4:7` or
obtained automatically using the `sct_label_vertebrae`
function (the file with the `labeled_discs.nii.gz`
suffix).
Example: `t2s_discs.nii.gz`.
OPTIONAL ARGUMENTS:
-num-of-slices <int> Number of additional axial slices above and below the
intervertebral disc to process.
Specifying `-num-of-slices 1` will process 3 slices
total per disc (+/- 1), `2` will process 5 slices total
(+/- 2), and so on.
(default: 0)
-angle-corr <int> Angle correction for computing morphometric measures.
When angle correction is used, the cord within the slice
is stretched/expanded by a factor corresponding to the
cosine of the angle between the centerline and the axial
plane. If the cord is already quasi-orthogonal to the
slab, you can set `-angle-corr` to 0.
(default: 1)
-o <file> Output CSV file name. If not provided, the suffix
`compression_results` is added to the file name provided
by the flag `-s`.
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_detect_pmj¶
--
Spinal Cord Toolbox (7.0)
sct_detect_pmj -h
--
usage: sct_detect_pmj -i <file> -c {t1,t2} [-s <file>] [-ofolder <folder>]
[-o <file>] [-qc <str>] [-qc-dataset <str>]
[-qc-subject <str>] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
[-r {0,1}]
Detection of the Ponto-Medullary Junction (PMJ). This method is based on a
machine-learning algorithm published in (Gros et al. 2018, Medical Image
Analysis, https://doi.org/10.1016/j.media.2017.12.001). Two models are
available: one for T1w-like and another for T2w-like images. If the PMJ is
detected from the input image, a NIfTI mask is output ("*_pmj.nii.gz") with one
voxel (value=50) located at the predicted PMJ position. If the PMJ is not
detected, nothing is output.
MANDATORY ARGUMENTS:
-i <file> Input image. Example: `t2.nii.gz`
-c {t1,t2} Type of image contrast, if your contrast is not in the
available options (t1, t2), use t1 (cord bright/ CSF
dark) or t2 (cord dark / CSF bright)
OPTIONAL ARGUMENTS:
-s <file> SC segmentation or centerline mask. Provide this mask
helps the detection of the PMJ by indicating the
position of the SC in the Right-to-Left direction.
Example: `t2_seg.nii.gz`
-ofolder <folder> Output folder. Example: `My_Output_Folder`
-o <file> Output filename. Example: `pmj.nii.gz`
-qc <str> The path where the quality control generated content
will be saved.
-qc-dataset <str> If provided, this string will be mentioned in the QC
report as the dataset the process was run on.
-qc-subject <str> If provided, this string will be mentioned in the QC
report as the subject the process was run on.
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_dice_coefficient¶
--
Spinal Cord Toolbox (7.0)
sct_dice_coefficient -h
--
usage: sct_dice_coefficient -i <file> -d <file> [-2d-slices {0,1,2}] [-b <list>]
[-bmax {0,1}] [-bzmax {0,1}] [-bin {0,1}] [-o <str>]
[-h] [-v <int>] [-profile-time [<file>]]
[-trace-memory [<folder>]] [-r {0,1}]
Compute the Dice Coefficient. N.B.: indexing (in both time and space) starts
with 0 not 1! Inputting `-1` for a size will set it to the full image extent for
that dimension.
MANDATORY ARGUMENTS:
-i <file> First input image. Example: `t2_seg.nii.gz`
-d <file> Second input image. Example: `t2_manual_seg.nii.gz`
OPTIONAL ARGUMENTS:
-2d-slices {0,1,2} Compute DC on 2D slices in the specified dimension
-b <list> Bounding box with the coordinates of the origin and the
size of the box as follow:
x_origin,x_size,y_origin,y_size,z_origin,z_size.
Example: 5,10,5,10,10,15
-bmax {0,1} Use maximum bounding box of the images union to compute
DC.
-bzmax {0,1} Use maximum bounding box of the images union in the "Z"
direction to compute DC.
-bin {0,1} Binarize image before computing DC. (Put non-zero-voxels
to 1)
-o <str> Output file with DC results (.txt). Example:
`dice_coeff.txt`
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_dmri_compute_bvalue¶
--
Spinal Cord Toolbox (7.0)
sct_dmri_compute_bvalue -h
--
usage: sct_dmri_compute_bvalue -g <float> -b <float> -d <float> [-h] [-v <int>]
[-profile-time [<file>]]
[-trace-memory [<folder>]]
Calculate b-value (in mm^2/s).
MANDATORY ARGUMENTS:
-g <float> Amplitude of diffusion gradients (in mT/m). Example:
`40`
-b <float> Big delta: time between both diffusion gradients (in
ms). Example: `40`
-d <float> Small delta: duration of each diffusion gradient (in
ms). Example: `30`
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_dmri_compute_dti¶
--
Spinal Cord Toolbox (7.0)
sct_dmri_compute_dti -h
--
usage: sct_dmri_compute_dti -i <file> -bval <file> -bvec <file>
[-method {standard,restore}] [-evecs {0,1}]
[-m <file>] [-o <str>] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
Compute Diffusion Tensor Images (DTI) using dipy.
MANDATORY ARGUMENTS:
-i <file> Input 4d file. Example: `dmri.nii.gz`
-bval <file> Bvals file. Example: `bvals.txt`
-bvec <file> Bvecs file. Example: `bvecs.txt`
OPTIONAL ARGUMENTS:
-method {standard,restore}
Type of method to calculate the diffusion tensor:
- `standard:` Standard equation [Basser, Biophys J
1994]
- `restore`: Robust fitting with outlier detection
[Chang, MRM 2005]
(default: standard)
-evecs {0,1} Output tensor eigenvectors and eigenvalues. (default: 0)
-m <file> Mask used to compute DTI in for faster processing.
Example: `mask.nii.gz`
-o <str> Output prefix. (default: dti_)
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_dmri_concat_bvals¶
--
Spinal Cord Toolbox (7.0)
sct_dmri_concat_bvals -h
--
usage: sct_dmri_concat_bvals -i <file> [<file> ...] [-o <file>] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
Concatenate bval files in time.
MANDATORY ARGUMENTS:
-i <file> [<file> ...]
List of the bval files to concatenate. Example:
`dmri_b700.bval dmri_b2000.bval`
OPTIONAL ARGUMENTS:
-o <file> Output file with bvals merged. Example:
`dmri_b700_b2000_concat.bval`
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_dmri_concat_bvecs¶
--
Spinal Cord Toolbox (7.0)
sct_dmri_concat_bvecs -h
--
usage: sct_dmri_concat_bvecs -i <file> [<file> ...] [-o <file>] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
Concatenate bvec files in time. You can either use bvecs in lines or columns.
N.B.: Return bvecs in lines. If you need it in columns, please use
sct_dmri_transpose_bvecs afterwards.
MANDATORY ARGUMENTS:
-i <file> [<file> ...]
List of the bvec files to concatenate. Example:
`dmri_b700.bvec dmri_b2000.bvec`
OPTIONAL ARGUMENTS:
-o <file> Output file with bvecs concatenated. Example:
`dmri_b700_b2000_concat.bvec`
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_dmri_denoise_patch2self¶
--
Spinal Cord Toolbox (7.0)
sct_dmri_denoise_patch2self -h
--
usage: sct_dmri_denoise_patch2self -i <file> -b <file>
[-model {ols,ridge,lasso}] [-radius <int>]
[-o <str>] [-h] [-v <int>]
[-profile-time [<file>]]
[-trace-memory [<folder>]]
Utility function to denoise diffusion MRI images. Returns the denoised image and
also the difference between the input and the output. The Patch2Self denoising
algorithm is based on self-supervised denoising via statistical independence of
noise, as described in the following publications:
- Fadnavis et al. Patch2Self: Denoising Diffusion MRI with Self-supervised
Learning. NeurIPS, 2020, Vol. 33. (https://arxiv.org/abs/2011.01355)
- Schilling et al. Patch2Self denoising of diffusion MRI in the cervical
spinal cord improves intra-cord contrast, signal modelling, repeatability,
and feature conspicuity. medRxiv, 2021.
(https://www.medrxiv.org/content/10.1101/2021.10.04.21264389v2)
The implementation is based on DIPY (https://docs.dipy.org/stable/examples_built
/preprocessing/denoise_patch2self.html).
MANDATORY ARGUMENTS:
-i <file> Input NIfTI image to be denoised. Example:
`image_input.nii.gz`
-b <file> Input bvals file corresponding to the NIfTI file to be
denoised. Example: `filename.bval`
OPTIONAL ARGUMENTS:
-model {ols,ridge,lasso}
Type of regression model used for self-supervised
training within Patch2Self. (default: ols)
-radius <int> Patch Radius used to generate p-neighbourhoods within
Patch2Self. Notes:
- A radius of `0` will use 1x1x1 p-neighbourhoods, a
radius of `1` will use 3x3x3 p-neighbourhoods, and
so on.
- For anisotropic patch sizes, provide a comma-
delimited list of 3 integers. (e.g. `-radius
0,1,0`). For isotropic patch sizes, provide a single
int value (e.g. `-radius 0`).
(default: 0)
-o <str> Name of the output NIFTI image.
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_dmri_display_bvecs¶
--
Spinal Cord Toolbox (7.0)
sct_dmri_display_bvecs -h
--
usage: sct_dmri_display_bvecs -bvec <file> [-bval <file>] [-h] [-v <int>]
[-profile-time [<file>]]
[-trace-memory [<folder>]]
Display scatter plot of gradient directions from bvecs file. If you have multi-
shell acquisition,you can provide also bvals file to display individual shells
in q-space.
MANDATORY ARGUMENTS:
-bvec <file> Input bvecs file. Example: `sub-001_dwi.bvec`
OPTIONAL ARGUMENTS:
-bval <file> Input bval file (for multi-shell acquisition). Example:
`sub-001_dwi.bval`
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_dmri_moco¶
--
Spinal Cord Toolbox (7.0)
sct_dmri_moco -h
--
usage: sct_dmri_moco -i <file> -bvec <file> [-bval <file>] [-bvalmin <float>]
[-g <int>] [-m <file>] [-param <list>]
[-x {nn,linear,spline}] [-ofolder <folder>] [-qc <folder>]
[-qc-seg <file>] [-qc-fps <float>] [-qc-dataset <str>]
[-qc-subject <str>] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
[-r {0,1}]
Motion correction of dMRI data. Some of the features to improve robustness were
proposed in Xu et al. (https://dx.doi.org/10.1016/j.neuroimage.2012.11.014) and
include:
- group-wise (`-g`)
- slice-wise regularized along z using polynomial function (-param). For more
info about the method, type: `isct_antsSliceRegularizedRegistration`
- masking (`-m`)
- iterative averaging of target volume
The outputs of the motion correction process are:
- the motion-corrected dMRI volumes
- the time average of the corrected dMRI volumes with b == 0
- the time average of the corrected dMRI volumes with b != 0
- a time-series with 1 voxel in the XY plane, for the X and Y motion direction
(two separate files), as required for FSL analysis.
- a TSV file with one row for each time point, with the slice-wise average of
the motion correction magnitude for that time point, that can be used for
Quality Control.
MANDATORY ARGUMENTS:
-i <file> Diffusion data. Example: `dmri.nii.gz`
-bvec <file> Bvecs file. Example: `bvecs.txt`
OPTIONAL ARGUMENTS:
-bval <file> Bvals file. Example: `bvals.txt`
-bvalmin <float> B-value threshold (in s/mm2) below which data is
considered as b=0. (default: 100)
-g <int> Group nvols successive dMRI volumes for more robustness.
(default: 3)
-m <file> Binary mask to limit voxels considered by the
registration metric. You may also provide a softmask
(nonbinary, [0, 1]), and it will be binarized at 0.5.
Example: `dmri_mask.nii.gz`
-param <list> Advanced parameters. Assign value with `=`, and separate
arguments with `,`.
- `poly` [int]: Degree of polynomial function used for
regularization along Z. For no regularization set to
0. Default=2.
- `smooth` [mm]: Smoothing kernel. Default=1.
- `metric` {MI, MeanSquares, CC}: Metric used for
registration. Default=MI.
- `gradStep` [float]: Searching step used by
registration algorithm. The higher the more
deformation allowed. Default=1.
- `sample` [None or 0-1]: Sampling rate used for
registration metric. Default=None.
-x {nn,linear,spline}
Final interpolation. (default: spline)
-ofolder <folder> Output folder.
-qc <folder> The path where the quality control generated content
will be saved. (Note: Both `-qc` and `-qc-seg` are
required in order to generate a QC report.)
-qc-seg <file> Segmentation of spinal cord to improve cropping in qc
report. (Note: Both `-qc` and `-qc-seg` are required in
order to generate a QC report.)
-qc-fps <float> This float number is the number of frames per second for
the output gif images. (default: 3)
-qc-dataset <str> If provided, this string will be mentioned in the QC
report as the dataset the process was run on.
-qc-subject <str> If provided, this string will be mentioned in the QC
report as the subject the process was run on.
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_dmri_separate_b0_and_dwi¶
--
Spinal Cord Toolbox (7.0)
sct_dmri_separate_b0_and_dwi -h
--
usage: sct_dmri_separate_b0_and_dwi -i <file> -bvec <file> [-a {0,1}]
[-bval <file>] [-bvalmin <float>]
[-ofolder <folder>] [-h] [-v <int>]
[-profile-time [<file>]]
[-trace-memory [<folder>]] [-r {0,1}]
Separate b=0 and DW images from diffusion dataset. The output files will have a
suffix (_b0 and _dwi) appended to the input file name.
MANDATORY ARGUMENTS:
-i <file> Diffusion data. Example: `dmri.nii.gz`
-bvec <file> Bvecs file. Example: `bvecs.txt`
OPTIONAL ARGUMENTS:
-a {0,1} Average b=0 and DWI data. 0 = no, 1 = yes (default: 1)
-bval <file> bvals file. Used to identify low b-values (in case
different from 0). Example: `bvals.txt`
-bvalmin <float> B-value threshold (in s/mm2) below which data is
considered as b=0. Example: `50.0`
-ofolder <folder> Output folder. (default: .)
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_dmri_transpose_bvecs¶
--
Spinal Cord Toolbox (7.0)
sct_dmri_transpose_bvecs -h
--
usage: sct_dmri_transpose_bvecs -bvec <file> [-o <file>] [-h] [-v <int>]
[-profile-time [<file>]]
[-trace-memory [<folder>]]
Transpose bvecs file (if necessary) to get nx3 structure.
MANDATORY ARGUMENTS:
-bvec <file> Input bvecs file. Example: `bvecs.txt`
OPTIONAL ARGUMENTS:
-o <file> Output bvecs file. By default, input file is
overwritten. Example: `bvecs_t.txt`
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_download_data¶
--
Spinal Cord Toolbox (7.0)
sct_download_data -h
--
usage: sct_download_data -d <dataset> [-o <folder>] [-k] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
Download binaries from the web.
MANDATORY ARGUMENTS:
-d <dataset> Name of the dataset, as listed in the table below. If
'default' is specified, then all default datasets will
be re-downloaded. (Default datasets are critical
datasets downloaded during installation.)
OPTIONAL ARGUMENTS:
-o <folder> Path to a directory to save the downloaded data.
(If not provided, the dataset will be downloaded to the
SCT installation directory by default. Directory will be
created if it does not exist. Warning: existing data in
the directory will be erased unless `-k` is provided.)
-k Keep existing data in destination directory. (default:
False)
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
DATASET NAME TYPE
--------------------------------------------------
binaries_linux Binaries
binaries_osx Binaries
binaries_win Binaries
[91msct_example_data [0mDatasets
[91msct_testing_data [0mDatasets
[91mdeepreg_models [0mModels
[91mdeepseg_gm_models [0mModels
[91mdeepseg_lesion_models [0mModels
[91mdeepseg_sc_models [0mModels
[91mmanual-correction [0mSCT Course Files
[91msct_course_data [0mSCT Course Files
[91mMNI-Poly-AMU [0mTemplates
[91mPAM50 [0mTemplates
[91mPAM50_normalized_metrics [0mTemplates
[91mexvivo_template [0mTemplates
[91mtemplate-dog [0mTemplates
Legend: [92minstalled[0m | [91mnot installed[0m (in the $SCT_DIR/data folder)
sct_extract_metric¶
--
Spinal Cord Toolbox (7.0)
sct_extract_metric -h
--
usage: sct_extract_metric -i <file> [-f <folder>] [-l <str>] [-list-labels]
[-method {ml,map,wa,bin,median,max}] [-append {0,1}]
[-combine {0,1}] [-o <file>] [-output-map <file>]
[-z <str>] [-perslice {0,1}] [-vert <str>]
[-vertfile <file>] [-perlevel <int>] [-param <str>]
[-fix-label <list>] [-norm-file <file>]
[-norm-method {sbs,whole}] [-mask-weighted <file>]
[-discard-neg-val {0,1}] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
This program extracts metrics (e.g., DTI or MTR) within labels. Labels could be
a single file or a folder generated with 'sct_warp_template' containing multiple
label files and a label description file (info_label.txt). The labels should be
in the same space coordinates as the input image.
The labels used by default are taken from the PAM50 template. To learn about the
available PAM50 white/grey matter atlas labels and their corresponding ID
values, please refer to:
https://spinalcordtoolbox.com/overview/concepts/pam50.html#white-and-grey-
matter-atlas-pam50-atlas
To compute FA within labels 0, 2 and 3 within vertebral levels C2 to C7 using
binary method:
`sct_extract_metric -i dti_FA.nii.gz -l 0,2,3 -vert 2:7 -method bin`
To compute average MTR in a region defined by a single label file (could be
binary or 0-1 weighted mask) between slices 1 and 4:
s`ct_extract_metric -i mtr.nii.gz -f my_mask.nii.gz -z 1:4 -method wa`
MANDATORY ARGUMENTS:
-i <file> Image file to extract metrics from. Example: `FA.nii.gz`
OPTIONAL ARGUMENTS:
-f <folder> Single label file, or folder that contains WM tract
labels. Example: /home/docs/checkouts/readthedocs.org/us
er_builds/spinalcordtoolbox/envs/stable/lib/python3.9/si
te-packages/data/PAM50/atlas (default: label/atlas)
-l <str> Label IDs to extract the metric from. Default = all
labels. Separate labels with `,`. To select a group of
consecutive labels use `:`. Example: `1:3` is equivalent
to `1,2,3`. Maximum Likelihood (or MAP) is computed
using all tracts, but only values of the selected tracts
are reported.
-list-labels List available labels. These labels are defined in the
file `info_label.txt` located in the folder specified by
the flag `-f`.
-method {ml,map,wa,bin,median,max}
Method to extract metrics.
- `ml`: maximum likelihood: This method is recommended
for large labels and low noise. Also, this method
should only be used with the PAM50 white/gray matter
atlas, or with any custom atlas as long as the sum
across all labels equals 1, in each voxel part of the
atlas.
- `map`: maximum a posteriori: Mean priors are
estimated by maximum likelihood within three clusters
(white matter, gray matter and CSF). Tract and noise
variance are set with flag `-p`. This method should
only be used with the PAM50 white/gray matter atlas,
or with any custom atlas as long as the sum across all
labels equals 1, in each voxel part of the atlas.
- `wa`: weighted average
- `bin`: binarize mask (threshold=0.5)
- `median`: weighted median: This implementation of
the median treats quantiles as a continuous (vs.
discrete) function. For more details, see
https://pypi.org/project/wquantiles/
- `max`: for each z-slice of the input data, extract
the max value for each slice of the input data.
(default: wa)
-append {0,1} Whether to append results as a new line in the output
csv file instead of overwriting it. 0 = no, 1 = yes
(default: 0)
-combine {0,1} Whether to combine multiple labels into a single
estimation. `0` = no, `1` = yes (default: 0)
-o <file> File name of the output result file collecting the
metric estimation results. Include the `.csv` file
extension in the file name. Example:
`extract_metric.csv` (default: extract_metric.csv)
-output-map <file> File name for an image consisting of the atlas labels
multiplied by the estimated metric values yielding the
metric value map, useful to assess the metric estimation
and especially partial volume effects.
-z <str> Slice range to estimate the metric from. First slice is
0. Example: `5:23`
You can also select specific slices using commas.
Example: `0,2,3,5,12`
-perslice {0,1} Whether to output one metric per slice instead of a
single output metric. `0` = no, `1` = yes.
Please note that when methods ml or map are used,
outputting a single metric per slice and then averaging
them all is not the same as outputting a single metric
at once across all slices.
-vert <str> Vertebral levels to compute the metrics across. Example:
`2:9` for C2 to T2. If you also specify a range of
slices with flag `-z`, the intersection between the
specified slices and vertebral levels will be
considered.
-vertfile <file> Vertebral labeling file. Only use with flag `-vert`.
The input Image and the vertebral labelling file must in
the same voxel coordinate system and must match the
dimensions between each other.
(default: ./label/template/PAM50_levels.nii.gz)
-perlevel <int> Whether to output one metric per vertebral level instead
of a single output metric. `0` = no, `1` = yes.
Please note that this flag needs to be used with the
-vert option.
(default: 0)
FOR ADVANCED USERS:
-param <str> Advanced parameters for the `map` method. All values
must be provided, and separated with `,`.
- First value: standard deviation of metrics across
labels
- Second value: standard deviation of the noise
(assumed Gaussian)
-fix-label <list> When using ML or MAP estimations, if you do not want to
estimate the metric in one label and fix its value to
avoid effects on other labels, specify
<label_ID>,<metric_value. Example: -fix-label 36,0 (Fix
the CSF value)
-norm-file <file> Filename of the label by which the user wants to
normalize.
-norm-method {sbs,whole}
Method to use for normalization:
- `sbs`: normalization slice-by-slice
- `whole`: normalization by the metric value in the
whole label for all slices.
-mask-weighted <file>
Nifti mask to weight each voxel during ML or MAP
estimation. Example: PAM50_wm.nii.gz
-discard-neg-val {0,1}
Whether to discard voxels with negative value when
computing metrics statistics. 0 = no, 1 = yes (default:
0)
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_flatten_sagittal¶
--
Spinal Cord Toolbox (7.0)
sct_flatten_sagittal -h
--
usage: sct_flatten_sagittal -i <file> -s <file> [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
Flatten the spinal cord such within the medial sagittal plane. Useful to make
nice pictures. Output data has suffix _flatten. Output type is float32
(regardless of input type) to minimize loss of precision during conversion.
MANDATORY ARGUMENTS:
-i <file> Input volume. Example: `t2.nii.gz`
-s <file> Spinal cord segmentation or centerline. Example:
`t2_seg.nii.gz`
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_fmri_compute_tsnr¶
--
Spinal Cord Toolbox (7.0)
sct_fmri_compute_tsnr -h
--
usage: sct_fmri_compute_tsnr -i <file> [-m <file>] [-o <file>] [-qc <str>]
[-qc-dataset <str>] [-qc-subject <str>] [-h]
[-v <int>] [-profile-time [<file>]]
[-trace-memory [<folder>]]
Compute temporal SNR (tSNR) in fMRI time series.
MANDATORY ARGUMENTS:
-i <file> Input fMRI data. Example: `fmri.nii.gz`
OPTIONAL ARGUMENTS:
-m <file> Binary (or weighted) mask within which tSNR will be
averaged. Example: `fmri_moco_mean_seg.nii.gz`
-o <file> tSNR data output file. Example: `fmri_tsnr.nii.gz`
-qc <str> The path where the quality control generated content
will be saved. Note: The `-m` parameter is required to
generate the QC report, as it is necessary to center the
QC on the region of interest.
-qc-dataset <str> If provided, this string will be mentioned in the QC
report as the dataset the process was run on
-qc-subject <str> If provided, this string will be mentioned in the QC
report as the subject the process was run on
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_fmri_moco¶
--
Spinal Cord Toolbox (7.0)
sct_fmri_moco -h
--
usage: sct_fmri_moco -i <file> [-g <int>] [-m <file>] [-param <list>]
[-ofolder <folder>] [-x {nn,linear,spline}] [-qc <folder>]
[-qc-seg <file>] [-qc-fps <float>] [-qc-dataset <str>]
[-qc-subject <str>] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
[-r {0,1}]
Motion correction of fMRI data. Some robust features include:
- group-wise (`-g`)
- slice-wise regularized along z using polynomial function (`-p`). For more
info about the method, type: `isct_antsSliceRegularizedRegistration`
- masking (`-m`)
- iterative averaging of target volume
The outputs of the motion correction process are:
- the motion-corrected fMRI volumes
- the time average of the corrected fMRI volumes
- a time-series with 1 voxel in the XY plane, for the X and Y motion direction
(two separate files), as required for FSL analysis.
- a TSV file with one row for each time point, with the slice-wise average of
the motion correction magnitude for that time point, that can be used for
Quality Control.
MANDATORY ARGUMENTS:
-i <file> Input data (4D). Example: `fmri.nii.gz`
OPTIONAL ARGUMENTS:
-g <int> Group nvols successive fMRI volumes for more robustness.
-m <file> Binary mask to limit voxels considered by the
registration metric. You may also provide a softmask
(nonbinary, [0, 1]), and it will be binarized at 0.5.
-param <list> Advanced parameters. Assign value with "="; Separate
arguments with ",".
- poly [int]: Degree of polynomial function used for
regularization along Z. For no regularization set to
0. Default=2.
- smooth [mm]: Smoothing kernel. Default=0.
- iter [int]: Number of iterations. Default=10.
- metric {MI, MeanSquares, CC}: Metric used for
registration. Default=MeanSquares.
- gradStep [float]: Searching step used by
registration algorithm. The higher the more
deformation allowed. Default=1.
- sampling [None or 0-1]: Sampling rate used for
registration metric. Default=None.
- numTarget [int]: Target volume or group (starting
with 0). Default=0.
- iterAvg [int]: Iterative averaging: Target volume is
a weighted average of the previously-registered
volumes. Default=1.
-ofolder <folder> Output path. (default: .)
-x {nn,linear,spline}
Final interpolation. (default: linear)
-qc <folder> The path where the quality control generated content
will be saved. (Note: Both `-qc` and `-qc-seg` are
required in order to generate a QC report.)
-qc-seg <file> Segmentation of spinal cord to improve cropping in qc
report. (Note: Both `-qc` and `-qc-seg` are required in
order to generate a QC report.)
-qc-fps <float> This float number is the number of frames per second for
the output gif images. (default: 3)
-qc-dataset <str> If provided, this string will be mentioned in the QC
report as the dataset the process was run on.
-qc-subject <str> If provided, this string will be mentioned in the QC
report as the subject the process was run on.
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_get_centerline¶
--
Spinal Cord Toolbox (7.0)
sct_get_centerline -h
--
usage: sct_get_centerline -i <file> [-method {optic,viewer,fitseg}]
[-c {t1,t2,t2s,dwi}]
[-centerline-algo {polyfit,bspline,linear,nurbs}]
[-centerline-smooth <int>] [-centerline-soft <int>]
[-space <str>] [-extrapolation <int>] [-o <file>]
[-gap <float>] [-qc <folder>] [-qc-dataset <str>]
[-qc-subject <str>] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
[-r {0,1}]
This function extracts the spinal cord centerline. Three methods are available:
'optic' (automatic), 'viewer' (manual), and 'fitseg' (applied on segmented
image). These functions output (i) a NIFTI file with labels corresponding to the
discrete centerline, and (ii) a csv file containing the float (more precise)
coordinates of the centerline in the RPI orientation.
Reference: C Gros, B De Leener, et al. Automatic spinal cord localization,
robust to MRI contrast using global curve optimization (2017).
doi.org/10.1016/j.media.2017.12.001
MANDATORY ARGUMENTS:
-i <file> Input image. Example: `t1.nii.gz`
OPTIONAL ARGUMENTS:
-method {optic,viewer,fitseg}
Method used for extracting the centerline.
- `optic`: automatic spinal cord detection method
- `viewer`: manual selection a few points followed by
interpolation
- `fitseg`: fit a regularized centerline on an
already-existing cord segmentation. This method will
interpolate if any slices are missing. Also, if
`-extrapolation 1` is specified, this method will
extrapolate beyond the segmentation boundaries (i.e.,
every axial slice will exhibit a centerline pixel).
(default: optic)
-c {t1,t2,t2s,dwi} Type of image contrast. Only relevant with `-method
optic`.
-centerline-algo {polyfit,bspline,linear,nurbs}
Algorithm for centerline fitting. Only relevant with
`-method fitseg`. (default: bspline)
-centerline-smooth <int>
Degree of smoothing for centerline fitting. Only
relevant with `-centerline-algo {bspline, linear}`.
(default: 30)
-centerline-soft <int>
Binary or soft centerline. `0` = binarized, `1` = soft.
Only relevant with `-method fitseg`. (default: 0)
-space <str> The coordinate space to use for units when outputting
the centerline coordinates to a .csv file.'pix'=pixel
dimensions, 'phys'=physical dimensions. (default: pix)
-extrapolation <int> Extrapolate beyond the segmentation boundaries. `0` = no
extrapolation, `1` = extrapolation. Only relevant with
`-method fitseg`.Note: `-extrapolation 1` works best
with lower-order (linear, nurbs) centerline fitting
algorithms (default: 0)
-o <file> File name for the centerline output file. If file
extension is not provided, `.nii.gz` will be used by
default. If `-o` is not provided, then the output file
will be the input with suffix `_centerline`. Example:
`centerline_optic.nii.gz`
-gap <float> Gap in mm between manually selected points. Only with
method=viewer. (default: 20.0)
-qc <folder> The path where the quality control generated content
will be saved.
-qc-dataset <str> If provided, this string will be mentioned in the QC
report as the dataset the process was run on.
-qc-subject <str> If provided, this string will be mentioned in the QC
report as the subject the process was run on.
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_image¶
--
Spinal Cord Toolbox (7.0)
sct_image -h
--
usage: sct_image -i <file> [<file> ...] [-o <file>] [-pad <list>]
[-pad-asym <list>] [-split {x,y,z,t}] [-concat {x,y,z,t}]
[-stitch] [-qc <folder>] [-qc-dataset <str>]
[-qc-subject <str>] [-remove-vol <list>] [-keep-vol <list>]
[-type {uint8,int16,int32,float32,complex64,float64,int8,uint16,uint32,int64,uint64}]
[-header [{sct,fslhd,nibabel}]] [-copy-header <file>]
[-set-sform-to-qform | -set-qform-to-sform] [-getorient]
[-setorient {LAS,LAI,LPS,LPI,LSA,LSP,LIA,LIP,RAS,RAI,RPS,RPI,RSA,RSP,RIA,RIP,ALS,ALI,ARS,ARI,ASL,ASR,AIL,AIR,PLS,PLI,PRS,PRI,PSL,PSR,PIL,PIR,SLA,SLP,SRA,SRP,SAL,SAR,SPL,SPR,ILA,ILP,IRA,IRP,IAL,IAR,IPL,IPR}]
[-flip {x,y,z,t}] [-transpose ax1,ax2,ax3] [-mcs] [-omc]
[-display-warp] [-to-fsl [<file> ...]] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
Perform manipulations on images (e.g., pad, change space, split along
dimension). Inputs can be a number, a 4d image, or several 3d images separated
with `,`
MANDATORY ARGUMENTS:
-i <file> [<file> ...]
Input file(s). Example: `data.nii.gz`
Note: Only `-concat`, `-omc` or `-stitch` support
multiple input files. In those cases, separate filenames
using spaces. Example usage: `sct_image -i data1.nii.gz
data2.nii.gz -concat`
OPTIONAL ARGUMENTS:
-o <file> Output file. Example: `data_pad.nii.gz`
IMAGE OPERATIONS:
-pad <list> Pad 3D image. Specify padding as: `x,y,z` (in voxel).
Example: `0,0,1`
-pad-asym <list> Pad 3D image with asymmetric padding. Specify padding
as: `x_i,x_f,y_i,y_f,z_i,z_f` (in voxel). Example:
`0,0,5,10,1,1`
-split {x,y,z,t} Split data along the specified dimension. The suffix
_DIM+NUMBER will be added to the intput file name.
-concat {x,y,z,t} Concatenate data along the specified dimension
-stitch Stitch multiple images acquired in the same orientation
utilizing the algorithm by Lavdas, Glocker et al.
(https://doi.org/10.1016/j.crad.2019.01.012). (default:
False)
-qc <folder> The path where the quality control generated content
will be saved. (Note: QC reporting is only available for
`sct_image -stitch`).
-qc-dataset <str> If provided, this string will be mentioned in the QC
report as the dataset the process was run on. (Note: QC
reporting is only available for `sct_image -stitch`).
-qc-subject <str> If provided, this string will be mentioned in the QC
report as the subject the process was run on. (Note: QC
reporting is only available for `sct_image -stitch`).
-remove-vol <list> Remove specific volumes from a 4d volume. Separate with
`,`. Example: `0,5,10`
-keep-vol <list> Keep specific volumes from a 4d volume (remove others).
Separate with `,`. Example: `1,2,3,11`
-type {uint8,int16,int32,float32,complex64,float64,int8,uint16,uint32,int64,uint64}
Change file type
HEADER OPERATIONS:
-header [{sct,fslhd,nibabel}]
Print the header of a NIfTI file. You can select the
output format of the header: 'sct' (default), 'nibabel'
or 'fslhd'.
-copy-header <file> Copy the NIfTI header of the source image (specified in
`-i`) to the destination image (specified here) and save
it into a new image (specified in `-o`).
!! WARNING: This command should ONLY be run to fix a
wrong header (e.g., where the qform and/or sform between
an image and a mask of the image do not match). Also
note that the image is NOT affected by this command, so
if the dimensions of the source and destination images
do not match, then you should probably NOT use this
command.
-set-sform-to-qform Set the input image's sform matrix equal to its qform
matrix. Use this option when you need to enforce
matching sform and qform matrices. This option can be
used by itself, or in combination with other functions.
(default: False)
-set-qform-to-sform Set the input image's qform matrix equal to its sform
matrix. Use this option when you need to enforce
matching sform and qform matrices. This option can be
used by itself, or in combination with other functions.
(default: False)
ORIENTATION OPERATIONS:
-getorient Get orientation of the input image (default: False)
-setorient {LAS,LAI,LPS,LPI,LSA,LSP,LIA,LIP,RAS,RAI,RPS,RPI,RSA,RSP,RIA,RIP,ALS,ALI,ARS,ARI,ASL,ASR,AIL,AIR,PLS,PLI,PRS,PRI,PSL,PSR,PIL,PIR,SLA,SLP,SRA,SRP,SAL,SAR,SPL,SPR,ILA,ILP,IRA,IRP,IAL,IAR,IPL,IPR}
Set orientation of the input image (modifies BOTH the
header and data array, similar to `fslswapdim`).
-flip {x,y,z,t} Flip an axis of the image's data array. (This will not
change the header orientation string.)
- WARNING: This option should only be used to fix the
data array when it does not match the orientation
string in the header. We recommend that you
investigate and understand where the mismatch
originated from in the first place before using this
option.
- Example: For an image with 'RPI' in its header,
`-flip x` will flip the LR axis of the data array.
-transpose ax1,ax2,ax3
Transpose the axes (x,y,z) of the image's data array.
(This will not change the header orientation string.)
- WARNING: This option should only be used to fix the
data array when it does not match the orientation
string in the header. We recommend that you
investigate and understand where the mismatch
originated from in the first place before using this
option.
- Example: For a 3D image with 'RPI' in its header,
`-transpose z,y,x` will swap the LR and SI axes of
the data array.
MULTI-COMPONENT OPERATIONS ON ITK COMPOSITE WARPING FIELDS:
-mcs Multi-component split: Split ITK warping field into
three separate displacement fields. The suffixes `_X`,
`_Y` and `_Z` will be added to the input file name.
(default: False)
-omc Multi-component merge: Merge inputted images into one
multi-component image. Requires several inputs.
(default: False)
WARPING FIELD OPERATIONS:
-display-warp Create a grid and deform it using provided warping
field. (default: False)
-to-fsl [<file> ...] Transform displacement field values to absolute FSL
warps. To be used with FSL's applywarp function with the
`--abs` flag. Input the file that will be used as the
input (source) for applywarp and optionally the target
(ref). The target file is necessary for the case where
the warp is in a different space than the target. For
example, the inverse warps generated by
`sct_straighten_spinalcord`. This feature has not been
extensively validated so consider checking the results
of `applywarp` against `sct_apply_transfo` before using
in FSL pipelines. Example syntax: `sct_image -i
WARP_SRC2DEST -to-fsl IM_SRC (IM_DEST) -o WARP_FSL`,
followed by FSL: `applywarp -i IM_SRC -r IM_DEST -w
WARP_FSL --abs -o IM_SRC2DEST`
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_label_utils¶
--
Spinal Cord Toolbox (7.0)
sct_label_utils -h
--
usage: sct_label_utils [-i <file>] [-o <file>] [-ilabel <file>]
(-add <int> | -create <list> | -create-add <list> | -create-seg <list> | -create-seg-mid <int> | -create-viewer <list> | -cubic-to-point | -disc <file> | -project-centerline <file> | -display | -increment | -vert-body <list> | -vert-continuous | -MSE <file> | -remove-reference <file> | -remove-sym <file> | -remove <list> | -keep <list>)
[-msg <str>] [-qc <folder>] [-qc-dataset <str>]
[-qc-subject <str>] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
Utility functions for label images.
REQUIRED I/O:
-i <file> Input image (Required) Example: `t2_labels.nii.gz`
OPTIONAL I/O:
-o <file> Output image. Note: Only some label utilities create an
output image. (default: labels.nii.gz)
-ilabel <file> File that contain labels that you want to correct. It is
possible to add new points with this option. Use with
`-create-viewer`. Example: `t2_labels_auto.nii.gz`
LABEL FUNCTIONS:
-add <int> Add value to all labels. Value can be negative.
-create <list> Create labels in a new image. List labels as:
x1,y1,z1,value1:x2,y2,z2,value2. Example:
12,34,32,1:12,35,33,2
-create-add <list> Same as `-create`, but add labels to the input image
instead of creating a new image. Example:
12,34,32,1:12,35,33,2
-create-seg <list> Create labels on a cord segmentation (or centerline)
image defined by `-i`. Each label should be specified
using the form `v1,v2` where `v1` is value of the slice
index along the inferior-superior axis, and `v2` is the
value of the label. Separate each label with `:`.
Example: `-create-seg 5,1:14,2:23,3` adds three labels
at the axial slices 5, 14, and 23 (starting from the
most inferior slice).
-create-seg-mid <int>
Similar to `-create-seg`. This option takes a single
label value, and will automatically select the mid-point
slice in the inferior-superior direction (so there is no
need for a slice index).
This is useful for when you have centered the field of
view of your data at a specific location. For example,
if you already know that the C2-C3 disc is centered in
the I-S direction, then you can enter `-create-seg-mid
3` for that label. This saves you the trouble of having
to manually specify a slice index using `-create-seg`.
-create-viewer <list>
Manually label from a GUI a list of labels IDs. Provide
a comma-separated list containing individual values
and/or intervals. Example: `-create-viewer 1:4,6,8` will
allow you to add labels [1,2,3,4,6,8] using the GUI.
-cubic-to-point Compute the center-of-mass for each label value.
(default: False)
-disc <file> Project disc labels (`-disc`) onto a spinal cord
segmentation (`-i`) within the axial plane to create a
labeled segmentation.
- Note: Unlike `sct_label_vertebrae -discfile`, this
function does NOT involve cord straightening.
- Note: This method does NOT involve orthogonal
projection onto the cord centerline. Details: https://gi
thub.com/spinalcordtoolbox/spinalcordtoolbox/issues/3395
#issuecomment-1478435265
The disc labeling follows the convention: https://spinal
cordtoolbox.com/user_section/tutorials/vertebral-
labeling/labeling-conventions.html
-project-centerline <file>
Project disc labels onto the spinal cord centerline.
-display Display all labels (i.e. non-zero values). (default:
False)
-increment Takes all non-zero values, sort them along the inverse z
direction, and attributes the values 1, 2, 3, etc.
(default: False)
-vert-body <list> From vertebral labeling, create points that are centered
at the mid-vertebral levels. Separate desired levels
with `,`. Example: `3,8`
To get all levels, enter 0.
-vert-continuous Convert discrete vertebral labeling to continuous
vertebral labeling. (default: False)
-MSE <file> Compute Mean Square Error between labels from input and
reference image. Specify reference image here.
-remove-reference <file>
Remove labels from input image (`-i`) that are not in
reference image (specified here).
-remove-sym <file> Remove labels from input image (`-i`) and reference
image (specified here) that don't match. You must
provide two output names separated by `,`.
-remove <list> Remove labels of specific value (specified here) from
reference image.
-keep <list> Keep labels of specific value (specified here) from
reference image.
OPTIONAL ARGUMENTS:
-msg <str> Display a message to explain the labeling task. Use with
-create-viewer
-qc <folder> The path where the quality control generated content
will be saved.
-qc-dataset <str> If provided, this string will be mentioned in the QC
report as the dataset the process was run on.
-qc-subject <str> If provided, this string will be mentioned in the QC
report as the subject the process was run on.
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_label_vertebrae¶
--
Spinal Cord Toolbox (7.0)
sct_label_vertebrae -h
--
usage: sct_label_vertebrae -i <file> -s <file> -c {t1,t2} [-t <folder>]
[-initz <list>] [-initcenter <int>]
[-initfile <file>] [-initlabel <file>]
[-discfile <file>] [-ofolder <file>]
[-laplacian <int>] [-clean-labels <int>]
[-scale-dist <float>] [-param <list>] [-qc <folder>]
[-qc-dataset <str>] [-qc-subject <str>] [-h]
[-v <int>] [-profile-time [<file>]]
[-trace-memory [<folder>]] [-r {0,1}]
This function takes an anatomical image and its cord segmentation (binary file),
and outputs the cord segmentation labeled with vertebral level. The algorithm
requires an initialization (first disc) and then performs a disc search in the
superior, then inferior direction, using template disc matching based on mutual
information score. The automatic method uses the module implemented in
'spinalcordtoolbox/vertebrae/detect_c2c3.py' to detect the C2-C3 disc.
MANDATORY ARGUMENTS:
-i <file> Input image. Example: `t2.nii.gz`
-s <file> Segmentation of the spinal cord. Example:
`t2_seg.nii.gz`
-c {t1,t2} Type of image contrast. 't2': cord dark / CSF bright.
't1': cord bright / CSF dark
OPTIONAL ARGUMENTS:
-t <folder> Path to template. (default: /home/docs/checkouts/readthe
docs.org/user_builds/spinalcordtoolbox/envs/stable/lib/p
ython3.9/site-packages/data/PAM50)
-initz <list> Initialize using slice number and disc value. Example:
`68,4` (slice 68 corresponds to disc C3/C4).
WARNING: Slice number should correspond to superior-
inferior direction (i.e. Z in RPI orientation, but Y in
LIP orientation).
-initcenter <int> Initialize using disc value centered in the rostro-
caudal direction. If the spine is curved, then consider
the disc that projects onto the cord at the center of
the z-FOV.
-initfile <file> Initialize labeling by providing a text file which
includes either `-initz` or `-initcenter` flag.
-initlabel <file> Initialize vertebral labeling by providing a nifti file
that has a single disc label. An example of such file is
a single voxel with value '3', which would be located at
the posterior tip of C2-C3 disc. Such label file can be
created using: `sct_label_utils -i IMAGE_REF -create-
viewer 3`; or by using the Python module 'detect_c2c3'
implemented in
'spinalcordtoolbox/vertebrae/detect_c2c3.py'.
-discfile <file> File with disc labels, which will be used to transform
the input segmentation into a vertebral level file. In
that case, there will be no disc detection. The
convention for disc labels is the following: value=3 ->
disc C2/C3, value=4 -> disc C3/C4, etc.
-ofolder <file> Output folder.
-laplacian <int> Apply Laplacian filtering. More accurate but could
mistake disc depending on anatomy. (default: 0)
-clean-labels <int> Clean output labeled segmentation to resemble original
segmentation. 0: no cleaning, 1: remove labeled voxels
that fall outside the original segmentation, 2: `-clean-
labels 1`, plus also fill in voxels so that the labels
cover the entire original segmentation. (default: 1)
-scale-dist <float> Scaling factor to adjust the average distance between
two adjacent intervertebral discs. For example, if you
are dealing with images from pediatric population, the
distance should be reduced, so you can try a scaling
factor of about 0.7. (default: 1.0)
-param <list> Advanced parameters. Assign value with `=`; Separate
arguments with `,`
- shift_AP `[mm]`: AP shift of centerline for disc
search
- size_AP `[mm]`: AP window size for disc search
- size_RL `[mm]`: RL window size for disc search
- size_IS `[mm]`: IS window size for disc search
(default: shift_AP=32,size_AP=11,size_RL=1,size_IS=19,s
hift_AP_visu=15)
-qc <folder> The path where the quality control generated content
will be saved.
-qc-dataset <str> If provided, this string will be mentioned in the QC
report as the dataset the process was run on.
-qc-subject <str> If provided, this string will be mentioned in the QC
report as the subject the process was run on.
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_maths¶
--
Spinal Cord Toolbox (7.0)
sct_maths -h
--
usage: sct_maths -i <file> -o <file> [-volumewise {0,1}] [-add [...]]
[-sub [...]] [-mul [...]] [-div [...]] [-mean {x,y,z,t}]
[-rms {x,y,z,t}] [-std {x,y,z,t}] [-bin <float>]
[-slicewise-mean {0,1,2}] [-otsu <int>] [-adap <list>]
[-otsu-median <list>] [-percent <int>] [-thr <float>]
[-uthr <float>] [-dilate <int>] [-erode <int>]
[-shape {square,cube,disk,ball}] [-dim {0,1,2}]
[-smooth <list>] [-laplacian <list>] [-denoise DENOISE]
[-mi <file>] [-minorm <file>] [-corr <file>]
[-symmetrize {0,1,2}]
[-type {uint8,int16,int32,float32,complex64,float64,int8,uint16,uint32,int64,uint64}]
[-h] [-v <int>] [-profile-time [<file>]]
[-trace-memory [<folder>]]
Perform mathematical operations on images.
MANDATORY ARGUMENTS:
-i <file> Input file. Example: `data.nii.gz`
-o <file> Output file. Example: `data_mean.nii.gz`
OPTIONAL ARGUMENTS:
-volumewise {0,1} Specifying this option will process a 4D image in a
"volumewise" manner:
- Split the 4D input into individual 3D volumes
- Apply the maths operations to each 3D volume
- Merge the processed 3D volumes back into a single 4D
output image
(default: 0)
BASIC OPERATIONS:
-add [ ...] Add following input. Can be a number or one or more
3D/4D images (separated with space). Examples:
- `sct_maths -i 3D.nii.gz -add 5`
(Result: 3D image with `5` added to each voxel)
- `sct_maths -i 3D.nii.gz -add 3D_2.nii.gz`
(Result: 3D image)
- `sct_maths -i 4D.nii.gz -add 4D_2.nii.gz`
(Result: 4D image)
- `sct_maths -i 4D_nii.gz -add 4D_2.nii.gz
4D_3.nii.gz` (Result: 4D image)
Note: If your terminal supports it, you can also specify
multiple images using a pattern:
- `sct_maths -i 4D.nii.gz -add 4D_*.nii.gz` (Result:
Adding `4D_2.nii.gz`, `4D_3.nii.gz`, etc.)
Note: If the input image is 4D, you can also leave
`-add` empty to sum the 3D volumes within the image:
- `sct_maths -i 4D.nii.gz -add` (Result: 3D image,
with 3D volumes summed within 4D image)
-sub [ ...] Subtract following input. Can be a number, or one or
more 3D/4D images (separated with space).
-mul [ ...] Multiply by following input. Can be a number, or one or
more 3D/4D images (separated with space). (See `-add`
for examples.)
-div [ ...] Divide by following input. Can be a number, or one or
more 3D/4D images (separated with space).
-mean {x,y,z,t} Average data across dimension.
-rms {x,y,z,t} Compute root-mean-squared across dimension.
-std {x,y,z,t} Compute STD across dimension.
-bin <float> Binarize image using specified threshold. Example: `0.5`
-slicewise-mean {0,1,2}
Compute slicewise mean the specified dimension. Zeros
are not inlcuded in the mean.
THRESHOLDING METHODS:
-otsu <int> Threshold image using Otsu algorithm (from skimage).
Specify the number of bins (e.g. 16, 64, 128)
-adap <list> Threshold image using Adaptive algorithm (from skimage).
Provide 2 values separated by `,` that correspond to the
parameters below. For example, `-adap 7,0` corresponds
to a block size of 7 and an offset of 0.
- Block size: Odd size of pixel neighborhood which is
used to calculate the threshold value.
- Offset: Constant subtracted from weighted mean of
neighborhood to calculate the local threshold value.
Suggested offset is 0.
-otsu-median <list> Threshold image using Median Otsu algorithm (from Dipy).
Provide 2 values separated by `,` that correspond to the
parameters below. For example, `-otsu-median 3,5`
corresponds to a filter size of 3 repeated over 5
iterations.
- Size: Radius (in voxels) of the applied median
filter.
- Iterations: Number of passes of the median filter.
-percent <int> Threshold image using percentile of its histogram.
-thr <float> Lower threshold limit (zero below number).
-uthr <float> Upper threshold limit (zero above number).
MATHEMATICAL MORPHOLOGY:
-dilate <int> Dilate binary or greyscale image with specified size. If
shape={'square', 'cube'}: size corresponds to the length
of an edge (size=1 has no effect). If shape={'disk',
'ball'}: size corresponds to the radius, not including
the center element (size=0 has no effect).
-erode <int> Erode binary or greyscale image with specified size. If
shape={'square', 'cube'}: size corresponds to the length
of an edge (size=1 has no effect). If shape={'disk',
'ball'}: size corresponds to the radius, not including
the center element (size=0 has no effect).
-shape {square,cube,disk,ball}
Shape of the structuring element for the mathematical
morphology operation. Default: `ball`.
If a 2D shape `{'disk', 'square'}` is selected, `-dim`
must be specified.
-dim {0,1,2} Dimension of the array which 2D structural element will
be orthogonal to. For example, if you wish to apply a 2D
disk kernel in the X-Y plane, leaving Z unaffected,
parameters will be: shape=disk, dim=2.
FILTERING METHODS:
-smooth <list> Gaussian smoothing filtering. Supply values for standard
deviations in mm. If a single value is provided, it will
be applied to each axis of the image. If multiple values
are provided, there must be one value per image axis.
(Examples: `-smooth 2.0,3.0,2.0` (3D image), `-smooth
2.0` (any-D image)).
-laplacian <list> Laplacian filtering. Supply values for standard
deviations in mm. If a single value is provided, it will
be applied to each axis of the image. If multiple values
are provided, there must be one value per image axis.
(Examples: `-laplacian 2.0,3.0,2.0` (3D image),
`-laplacian 2.0` (any-D image)).
-denoise DENOISE Non-local means adaptative denoising from P. Coupe et
al. as implemented in dipy. Separate with `,` Example:
`p=1,b=3`
- `p`: (patch radius) similar patches in the non-local
means are searched for locally, inside a cube of side
`2*p+1` centered at each voxel of interest. Default:
`p=1`
- `b`: (block radius) the size of the block to be used
(2*b+1) in the blockwise non-local means
implementation. Default: `b=5`.
Note, block radius must be smaller than the smaller
image dimension: default value is lowered for small
images)
To use default parameters, write `-denoise 1`
SIMILARITY METRIC:
-mi <file> Compute the mutual information (MI) between both input
files (`-i` and `-mi`) as in: https://scikit-learn.org/s
table/modules/generated/sklearn.metrics.mutual_info_scor
e.html
-minorm <file> Compute the normalized mutual information (MI) between
both input files (`-i` and `-mi`) as in: https://scikit-
learn.org/stable/modules/generated/sklearn.metrics.norma
lized_mutual_info_score.html
-corr <file> Compute the cross correlation (CC) between both input
files (`-i` and `-corr`).
MISC ARGUMENTS:
-symmetrize {0,1,2} Symmetrize data along the specified dimension.
-type {uint8,int16,int32,float32,complex64,float64,int8,uint16,uint32,int64,uint64}
Output type.
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_merge_images¶
--
Spinal Cord Toolbox (7.0)
sct_merge_images -h
--
usage: sct_merge_images -i <file> [<file> ...] -d <file> -w <file> [<file> ...]
[-x <str>] [-o <file>] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
[-r {0,1}]
Merge multiple source images (`-i`) onto destination space (`-d`). (All images
are warped to the destination space and then added together.)
To deal with overlap during merging (e.g. multiple input images map to the same
voxel regions in the destination space), the output voxels are divided by the
sum of the partial volume values for each image.
Specifically, the per-voxel calculation used is:
`im_out = (im_1*pv_1 + im_2*pv_2 + ...) / (pv_1 + pv_2 + ...)`
So this function acts like a weighted average operator, only in destination
voxels that share multiple source voxels.
MANDATORY ARGUMENTS:
-i <file> [<file> ...]
Input images
-d <file> Destination image
-w <file> [<file> ...]
List of warping fields from input images to destination
image
OPTIONAL ARGUMENTS:
-x <str> Interpolation for warping the input images to the
destination image. (default: linear)
-o <file> Output image (default: merged_images.nii.gz)
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_process_segmentation¶
--
Spinal Cord Toolbox (7.0)
sct_process_segmentation -h
--
usage: sct_process_segmentation -i <file> [-o <file>] [-append <int>] [-z <str>]
[-perslice <int>] [-vert <str>]
[-vertfile <str>] [-perlevel <int>]
[-angle-corr <int>]
[-angle-corr-centerline <str>]
[-centerline-algo {polyfit,bspline,linear,nurbs}]
[-centerline-smooth <int>] [-pmj <file>]
[-pmj-distance <float>] [-pmj-extent <float>]
[-normalize <list> [<list> ...]]
[-normalize-PAM50 <int>] [-qc <folder>]
[-qc-image <str>] [-qc-dataset <str>]
[-qc-subject <str>] [-h] [-v <int>]
[-profile-time [<file>]]
[-trace-memory [<folder>]] [-r {0,1}]
Compute the following morphometric measures based on the spinal cord
segmentation:
- area [mm^2]: Cross-sectional area, measured by counting pixels in each
slice. Partial volume can be accounted for by inputing a mask comprising
values within [0,1]. Can be normalized when specifying the flag `-normalize`
- angle_AP, angle_RL: Estimated angle between the cord centerline and the
axial slice. This angle is used to correct for morphometric information.
- diameter_AP, diameter_RL: Finds the major and minor axes of the cord and
measure their length.
- eccentricity: Eccentricity of the ellipse that has the same second-moments
as the spinal cord. The eccentricity is the ratio of the focal distance
(distance between focal points) over the major axis length. The value is in
the interval [0, 1). When it is 0, the ellipse becomes a circle.
- orientation: angle (in degrees) between the AP axis of the spinal cord and
the AP axis of the image
- solidity: CSA(spinal_cord) / CSA_convex(spinal_cord). The more ellipse-
shaped the cord is (i.e. the closer the perimeter of the cord is to being
fully convex), the closer the solidity ratio will be to 1. This metric is
interesting for detecting concave regions (e.g., in case of strong
compression).
- length: Length of the segmentation, computed by summing the slice thickness
(corrected for the centerline angle at each slice) across the specified
superior-inferior region.
IMPORTANT: There is a limit to the precision you can achieve for a given image
resolution. SCT does not truncate spurious digits when performing angle
correction, so please keep in mind that there may be non-significant digits in
the computed values. You may wish to compare angle-corrected values with their
corresponding uncorrected values to get a sense of the limits on precision.
To select the region to compute metrics over, choose one of the following
arguments:
1. `-z`: Select axial slices based on slice index.
2. `-pmj` + `-pmj-distance` + `-pmj-extent`: Select axial slices based on
distance from pontomedullary junction.
(For options 1 and 2, you can also add '-perslice' to compute metrics for
each axial slice, rather than averaging.)
3. `-vert` + `-vertfile`: Select a region based on vertebral labels instead
of individual slices.
(For option 3, you can also add `-perlevel` to compute metrics for each
vertebral level, rather than averaging.)
References:
- `-pmj`/`-normalize`:
Bédard S, Cohen-Adad J. Automatic measure and normalization of spinal cord
cross-sectional area using the pontomedullary junction. Frontiers in
Neuroimaging 2022.
https://doi.org/10.3389/fnimg.2022.1031253
- `-normalize-PAM50`:
Valošek J, Bédard S, Keřkovský M, Rohan T, Cohen-Adad J. A database of the
healthy human spinal cord morphometry in the PAM50 template space. Imaging
Neuroscience 2024; 2 1–15.
https://doi.org/10.1162/imag_a_00075
MANDATORY ARGUMENTS:
-i <file> Mask to compute morphometrics from. Could be binary or
weighted. E.g., spinal cord segmentation.Example:
seg.nii.gz
OPTIONAL ARGUMENTS:
-o <file> Output file name (add extension). (default: csa.csv)
-append <int> Append results as a new line in the output csv file
instead of overwriting it. (default: 0)
-z <str> Slice range to compute the metrics across. Example:
`5:23`
-perslice <int> Set to 1 to output one metric per slice instead of a
single output metric. Please note that when methods ml
or map is used, outputting a single metric per slice and
then averaging them all is not the same as outputting a
single metric at once across all slices. (default: 0)
-vert <str> Vertebral levels to compute the metrics across. Example:
2:9 for C2 to T2. If you also specify a range of slices
with flag `-z`, the intersection between the specified
slices and vertebral levels will be considered.
-vertfile <str> Vertebral labeling file. Only use with flag `-vert`.
The input and the vertebral labelling file must in the
same voxel coordinate system and must match the
dimensions between each other.
(default: ./label/template/PAM50_levels.nii.gz)
-perlevel <int> Set to 1 to output one metric per vertebral level
instead of a single output metric. This flag needs to be
used with flag `-vert`. (default: 0)
-angle-corr <int> Angle correction for computing morphometric measures.
When angle correction is used, the cord within the slice
is stretched/expanded by a factor corresponding to the
cosine of the angle between the centerline and the axial
plane. If the cord is already quasi-orthogonal to the
slab, you can set -angle-corr to 0. (default: 1)
-angle-corr-centerline <str>
Image to be used as a centerline for computing angle
correction (can be either a cord segmentation or a
single-voxel centerline mask). This argument is
optional; if not provided, the centerline will be
derived from the input segmentation. Use this option if
the input segmentation is irregularly shaped (e.g.
gray/white matter). In such a case, it is best to pass
the full cord segmentation to this option, as you will
get a more accurate centerline (and thus a more
accurate, consistent angle correction).
-centerline-algo {polyfit,bspline,linear,nurbs}
Algorithm for centerline fitting. Only relevant with
`-angle-corr 1`. (default: bspline)
-centerline-smooth <int>
Degree of smoothing for centerline fitting. Only use
with `-centerline-algo {bspline, linear}`. (default: 30)
-pmj <file> Ponto-Medullary Junction (PMJ) label file. Example:
`pmj.nii.gz`
-pmj-distance <float>
Distance (mm) from Ponto-Medullary Junction (PMJ) to the
center of the mask used to compute morphometric
measures. (To be used with flag `-pmj`.)
-pmj-extent <float> Extent (in mm) for the mask used to compute morphometric
measures. Each slice covered by the mask is included in
the calculation. (To be used with flag `-pmj` and `-pmj-
distance`.) (default: 20.0)
-normalize <list> [<list> ...]
Normalize CSA values ('MEAN(area)').
Two models are available:
1. sex, brain-volume, thalamus-volume.
2. sex, brain-volume.
Specify each value for the subject after the
corresponding predictor.
Example:
`-normalize sex 0 brain-volume 960606.0 thalamus-
volume 13942.0`
*brain-volume and thalamus-volume are in mm^3. For sex,
female: 0, male: 1.
The models were generated using T1w brain images from
804 healthy (non-pathological) participants ranging from
48 to 80 years old, taken from the UK Biobank dataset.
For more details on the subjects and methods used to
create the models, go to: https://github.com/sct-
pipeline/ukbiobank-spinalcord-csa#readme
Given the risks and lack of consensus surrounding CSA
normalization, we recommend thoroughly reviewing the
literature on this topic before applying this feature to
your data.
-normalize-PAM50 <int>
Set to 1 to bring the metrics in the PAM50 anatomical
dimensions perslice. `-vertfile` and `-perslice` need to
be specified. (default: 0)
-qc <folder> The path where the quality control generated content
will be saved. The QC report is only available for PMJ-
based CSA (with flag `-pmj`).
-qc-image <str> Input image to display in QC report. Typically, it would
be the source anatomical image used to generate the
spinal cord segmentation. This flag is mandatory if
using flag `-qc`.
-qc-dataset <str> If provided, this string will be mentioned in the QC
report as the dataset the process was run on.
-qc-subject <str> If provided, this string will be mentioned in the QC
report as the subject the process was run on.
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_propseg¶
--
Spinal Cord Toolbox (7.0)
sct_propseg -h
--
usage: sct_propseg -i <file> -c {t1,t2,t2s,dwi} [-o <file>] [-ofolder <folder>]
[-down <int>] [-up <int>] [-mesh] [-centerline-binary] [-CSF]
[-centerline-coord] [-cross] [-init-tube]
[-low-resolution-mesh] [-init-centerline <file>]
[-init <float>] [-init-mask <file>] [-mask-correction <file>]
[-rescale <float>] [-radius <float>] [-nbiter <int>]
[-max-area <float>] [-max-deformation <float>]
[-min-contrast <float>] [-d <float>]
[-distance-search <float>] [-alpha <float>] [-qc <folder>]
[-qc-dataset <str>] [-qc-subject <str>] [-correct-seg <int>]
[-h] [-v <int>] [-profile-time [<file>]]
[-trace-memory [<folder>]] [-r {0,1}]
This program segments automatically the spinal cord on T1- and T2-weighted
images, for any field of view. You must provide the type of contrast, the image
as well as the output folder path. The segmentation follows the spinal cord
centerline, which is provided by an automatic tool: Optic. The initialization of
the segmentation is made on the median slice of the centerline, and can be
adjusted using the `-init` parameter. The initial radius of the tubular mesh
that will be propagated should be adapted to size of the spinal cord on the
initial propagation slice.
Primary output is the binary mask of the spinal cord segmentation. This method
must provide VTK triangular mesh of the segmentation (option `-mesh`). Spinal
cord centerline is available as a binary image (`-centerline-binary`) or a text
file with coordinates in world referential (`-centerline-coord`).
Cross-sectional areas along the spinal cord can be available (`-cross`). Several
tips on segmentation correction can be found on the 'Correcting sct_propseg'
page in the Tutorials section of the documentation.
If the segmentation fails at some location (e.g. due to poor contrast between
spinal cord and CSF), edit your anatomical image (e.g. with fslview) and
manually enhance the contrast by adding bright values around the spinal cord for
T2-weighted images (dark values for T1-weighted). Then, launch the segmentation
again.
References:
- [De Leener B, Kadoury S, Cohen-Adad J. Robust, accurate and fast automatic
segmentation of the spinal cord. Neuroimage 98, 2014. pp 528-536. DOI:
10.1016/j.neuroimage.2014.04.051](https://pubmed.ncbi.nlm.nih.gov/24780696/)
- [De Leener B, Cohen-Adad J, Kadoury S. Automatic segmentation of the spinal
cord and spinal canal coupled with vertebral labeling. IEEE Trans Med Imaging.
2015 Aug;34(8):1705-18.](https://pubmed.ncbi.nlm.nih.gov/26011879/)
MANDATORY ARGUMENTS:
-i <file> Input image. Example: `ti.nii.gz`
-c {t1,t2,t2s,dwi} Type of image contrast. If your contrast is not in the
available options (t1, t2, t2s, dwi), use t1 (cord
bright / CSF dark) or t2 (cord dark / CSF bright)
OPTIONAL ARGUMENTS:
-o <file> Output filename. Example: `spinal_seg.nii.gz`
-ofolder <folder> Output folder.
-down <int> Down limit of the propagation. Default is 0.
-up <int> Up limit of the propagation. Default is the highest
slice of the image.
-mesh Output: mesh of the spinal cord segmentation (default:
False)
-centerline-binary Output: centerline as a binary image. (default: False)
-CSF Output: CSF segmentation. (default: False)
-centerline-coord Output: centerline in world coordinates. (default:
False)
-cross Output: cross-sectional areas. (default: False)
-init-tube Output: initial tubular meshes. (default: False)
-low-resolution-mesh Output: low-resolution mesh. (default: False)
-init-centerline <file>
Filename of centerline to use for the propagation. Use
format `.txt` or `.nii`; see file structure in
documentation.
Replace filename by `viewer` to use interactive viewer
for providing centerline. Example: `-init-centerline
viewer`
-init <float> Axial slice where the propagation starts, default is
middle axial slice.
-init-mask <file> Mask containing three center of the spinal cord, used to
initiate the propagation.
Replace filename by `viewer` to use interactive viewer
for providing mask. Example: `-init-mask viewer`
-mask-correction <file>
mask containing binary pixels at edges of the spinal
cord on which the segmentation algorithm will be forced
to register the surface. Can be used in case of
poor/missing contrast between spinal cord and CSF or in
the presence of artefacts/pathologies.
-rescale <float> Rescale the image (only the header, not the data) in
order to enable segmentation on spinal cords with
dimensions different than that of humans (e.g., mice,
rats, elephants, etc.). For example, if the spinal cord
is 2x smaller than that of human, then use `-rescale 2`
(default: 1.0)
-radius <float> Approximate radius (in mm) of the spinal cord. Default
is 4.
-nbiter <int> Stop condition (affects only the Z propogation): number
of iteration for the propagation for both direction.
Default is 200.
-max-area <float> [mm^2], stop condition (affects only the Z propogation):
maximum cross-sectional area. Default is 120.
-max-deformation <float>
[mm], stop condition (affects only the Z propogation):
maximum deformation per iteration. Default is 2.5
-min-contrast <float>
[intensity value], stop condition (affects only the Z
propogation): minimum local SC/CSF contrast, default is
50
-d <float> trade-off between distance of most promising point (d is
high) and feature strength (d is low), default depend on
the contrast. Range of values from 0 to 50. 15-25 values
show good results. Default is 10.
-distance-search <float>
maximum distance of optimal points computation along the
surface normals. Range of values from 0 to 30. Default
is 15
-alpha <float> Trade-off between internal (alpha is high) and external
(alpha is low) forces. Range of values from 0 to 50.
Default is 25.
-qc <folder> The path where the quality control generated content
will be saved.
-qc-dataset <str> If provided, this string will be mentioned in the QC
report as the dataset the process was run on.
-qc-subject <str> If provided, this string will be mentioned in the QC
report as the subject the process was run on.
-correct-seg <int> Enable (1) or disable (0) the algorithm that checks and
correct the output segmentation. More specifically, the
algorithm checks if the segmentation is consistent with
the centerline provided by isct_propseg. (default: 1)
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_qc¶
--
Spinal Cord Toolbox (7.0)
sct_qc -h
--
usage: sct_qc -i IMAGE -p
{sct_propseg,sct_deepseg_sc,sct_deepseg_gm,sct_deepseg_lesion,sct_register_multimodal,sct_register_to_template,sct_warp_template,sct_label_vertebrae,sct_detect_pmj,sct_label_utils,sct_get_centerline,sct_fmri_moco,sct_dmri_moco,sct_image_stitch,sct_fmri_compute_tsnr}
[-s SEG] [-d DEST] [-plane {axial,sagittal}] [-resample RESAMPLE]
[-text-labels {0,1}] [-qc QC] [-qc-dataset DATASET]
[-qc-subject SUBJECT] [-fps float] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
Generate Quality Control (QC) report following SCT processing.
MANDATORY ARGUMENTS:
-i IMAGE Input image #1
-p {sct_propseg,sct_deepseg_sc,sct_deepseg_gm,sct_deepseg_lesion,sct_register_multimodal,sct_register_to_template,sct_warp_template,sct_label_vertebrae,sct_detect_pmj,sct_label_utils,sct_get_centerline,sct_fmri_moco,sct_dmri_moco,sct_image_stitch,sct_fmri_compute_tsnr}
SCT function associated with the QC report to generate
OPTIONAL ARGUMENTS:
-s SEG Input segmentation or label
-d DEST Input image #2 to overlay on image #1 (requires a
segmentation), or output of another process. Example:
`sct_straighten_spinalcord`
-plane {axial,sagittal}
Plane of the output QC. Only relevant for `-p
sct_deepseg_lesion`.
-resample RESAMPLE Millimeter resolution to resample the image to. Set to 0
to turn off resampling. You can use this option to
control the zoom of the QC report: higher values will
result in smaller images, and lower values will result
in larger images.
-text-labels {0,1} If set to 0, text won't be drawn on top of labels. Only
relevant for `-p sct_label_vertebrae`. (default: 1)
-qc QC Path to save QC report. (default: ./qc)
-qc-dataset DATASET If provided, this string will be mentioned in the QC
report as the dataset the process was run on
-qc-subject SUBJECT If provided, this string will be mentioned in the QC
report as the subject the process was run on
-fps float The number of frames per second for output gif images.
Only useful for sct_fmri_moco and sct_dmri_moco.
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
Examples:
- `sct_qc -i t2.nii.gz -s t2_seg.nii.gz -p sct_deepseg_sc`
- `sct_qc -i t2.nii.gz -s t2_pmj.nii.gz -p sct_detect_pmj`
- `sct_qc -i t2.nii.gz -s t2_seg_labeled.nii.gz -p sct_label_vertebrae`
- `sct_qc -i t2.nii.gz -s t2_seg.nii.gz -p sct_deepseg_sc -qc-dataset mydata
-qc-subject sub-45`
- `sct_qc -i t2.nii.gz -s t2_seg.nii.gz -d t2_lesion.nii.gz -p
sct_deepseg_lesion -plane axial`
sct_register_multimodal¶
--
Spinal Cord Toolbox (7.0)
sct_register_multimodal -h
--
usage: sct_register_multimodal -i <file> -d <file> [-iseg <file>] [-dseg <file>]
[-ilabel <file>] [-dlabel <file>]
[-initwarp <file>] [-initwarpinv <file>]
[-m <file>] [-o <file>] [-owarp <file>]
[-owarpinv <file>] [-param <list>]
[-identity <int>] [-z <int>]
[-x {nn,linear,spline}] [-ofolder <folder>]
[-qc <folder>] [-qc-dataset <str>]
[-qc-subject <str>] [-h] [-v <int>]
[-profile-time [<file>]]
[-trace-memory [<folder>]] [-r {0,1}]
This program co-registers two 3D volumes. The deformation is non-rigid and is
constrained along Z direction (i.e., axial plane). Hence, this function assumes
that orientation of the destination image is axial (RPI). If you need to
register two volumes with large deformations and/or different contrasts, it is
recommended to input spinal cord segmentations (binary mask) in order to achieve
maximum robustness. The program outputs a warping field that can be used to
register other images to the destination image. To apply the warping field to
another image, use `sct_apply_transfo`
Tips:
- For a registration step using segmentations, use the MeanSquares metric.
Also, simple algorithm will be very efficient, for example centermass as a
'preregistration'.
- For a registration step using images of different contrast, use the Mutual
Information (MI) metric.
- Combine the steps by increasing the complexity of the transformation
performed in each step, for example:
```
-param step=1,type=seg,algo=slicereg,metric=MeanSquares:
step=2,type=seg,algo=affine,metric=MeanSquares,gradStep=0.2:
step=3,type=im,algo=syn,metric=MI,iter=5,shrink=2
```
- When image contrast is low, a good option is to perform registration only
based on the image segmentation, i.e. using type=seg
- Columnwise algorithm needs to be applied after a translation and rotation
such as centermassrot algorithm. For example:
```
-param step=1,type=seg,algo=centermassrot,metric=MeanSquares:
step=2,type=seg,algo=columnwise,metric=MeanSquares
```
MANDATORY ARGUMENTS:
-i <file> Image source. Example: `src.nii.gz`
-d <file> Image destination. Example: `dest.nii.gz`
OPTIONAL ARGUMENTS:
-iseg <file> Segmentation source. Example: `src_seg.nii.gz`
-dseg <file> Segmentation destination. Example: `dest_seg.nii.gz`
-ilabel <file> Labels source.
-dlabel <file> Labels destination.
-initwarp <file> Initial warping field to apply to the source image.
-initwarpinv <file> Initial inverse warping field to apply to the
destination image (only use if you wish to generate the
dest->src warping field)
-m <file> Mask that can be created with sct_create_mask to improve
accuracy over region of interest. This mask will be used
on the destination image. Masks will be binarized at
0.5. Example: `mask.nii.gz`
-o <file> Name of output file. Example: `src_reg.nii.gz`
-owarp <file> Name of output forward warping field.
-owarpinv <file> Name of output inverse warping field.
-param <list> Parameters for registration. Separate arguments with
`,`. Separate steps with `:`.
Example: step=1,type=seg,algo=slicereg,metric=MeanSquare
s:step=2,type=im,algo=syn,metric=MI,iter=5,shrink=2
- step: <int> Step number (starts at 1, except for
type=label).
- type: {im, seg, imseg, label} type of data used for
registration. If you specify 'im', you must also
provide arguments -i and -d. If you specify 'seg',
you must provide -iseg and -dseg. If you specify
imseg, you must provide all four arguments. If you
specify -label, you must provide -ilabel and
-dlabel. ((Note: Use type=label only at step=0. Use
type=imseg only for algo=centermassrot along with
rot_method=hog or rot_method=pca_hog.))
- algo: The algorithm used to compute the
transformation. Default=syn
* translation: translation in X-Y plane (2dof)
* rigid: translation + rotation in X-Y plane (4dof)
* affine: translation + rotation + scaling in X-Y
plane (6dof)
* syn: non-linear symmetric normalization
* bsplinesyn: syn regularized with b-splines
* slicereg: regularized translations (see:
goo.gl/Sj3ZeU)
* centermass: slicewise center of mass alignment
(seg only).
* centermassrot: slicewise center of mass and
rotation alignment using method specified in
'rot_method'
* columnwise: R-L scaling followed by A-P columnwise
alignment (seg only).
* dl: Contrast-agnostic, deep learning-based
registration based on the SynthMorph architecture.
Can be run using: -param step=1,type=im,algo=dl
- slicewise: <int> Slice-by-slice 2d transformation.
Default=0.
- metric: {CC, MI, MeanSquares}. Default=MeanSquares.
* CC: The cross correlation metric compares the
images based on their intensities but with a small
normalization. It can be used with images with the
same contrast (for ex. T2-w with T2-w). In this
case it is very efficient but the computation time
can be very long.
* MI: the mutual information metric compares the
images based on their entropy, therefore the
images need to be big enough to have enough
information. It works well for images with
different contrasts (for example T2-w with T1-w)
but not on segmentations.
* MeanSquares: The mean squares metric compares the
images based on their intensities. It can be used
only with images that have exactly the same
contrast (with the same intensity range) or with
segmentations.
- iter: <int> Number of iterations. Default=10.
- shrink: <int> Shrink factor. A shrink factor of 2
will down sample the images by a factor of 2 to do
the registration, and thus allow bigger deformations
(and be faster to compute). It is usually combined
with a smoothing. (only for syn/bsplinesyn).
Default=1.
- smooth: <int> Smooth factor (in mm). Note: if
algo={centermassrot,columnwise} the smoothing kernel
is: SxSx0. Otherwise it is SxSxS. Default=0.
- laplacian: <int> Laplace filter using Gaussian
second derivatives, applied before registration. The
input number correspond to the standard deviation of
the Gaussian filter. Default=0.
- gradStep: <float> The gradient step used by the
function opitmizer. A small gradient step can lead
to a more accurate registration but will take longer
to compute, with the risk to not reach convergence.
A bigger gradient step will make the registration
faster but the result can be far from an optimum.
Default=0.5.
- deformation: ?x?x?: Restrict deformation (for ANTs
algo). Replace ? by 0 (no deformation) or 1
(deformation). Default=1x1x0.
- init: Initial translation alignment based on:
* geometric: Geometric center of images
* centermass: Center of mass of images
* origin: Physical origin of images
- poly: <int> Polynomial degree of regularization
(only for algo=slicereg). Default=5.
- filter_size: <float> Filter size for regularization
(only for algo=centermassrot). Default=5.
- smoothWarpXY: <int> Smooth XY warping field (only
for algo=columnwize). Default=2.
- pca_eigenratio_th: <int> Min ratio between the two
eigenvalues for PCA-based angular adjustment (only
for algo=centermassrot and rot_method=pca).
Default=1.6.
- dof: <str> Degree of freedom for type=label.
Separate with `_`. Default=Tx_Ty_Tz_Rx_Ry_Rz. T
stands for translation, R stands for rotation, and S
stands for scaling. x, y, and z indicate the
direction. Examples:
* Tx_Ty_Tz_Rx_Ry_Rz would allow translation on x, y
and z axes and rotation on x, y and z axes
* Tx_Ty_Tz_Sz would allow translation on x, y and z
axes and scaling only on z axis
- rot_method {pca, hog, pcahog}: rotation method to be
used with algo=centermassrot. If using hog or
pcahog, type should be set to imseg. Default=pca
* pca: approximate cord segmentation by an ellipse
and finds it orientation using PCA's eigenvectors
* hog: finds the orientation using the symmetry of
the image
* pcahog: tries method pca and if it fails, uses
method hog.
-identity <int> Supplying this option will skip registration
optimization (e.g. translations, rotations,
deformations) and will only rely on the qform (from the
NIfTI header) of the source and destination images. Use
this option if you wish to put the source image into the
space of the destination image (i.e. match dimension,
resolution and orientation). (default: 0)
-z <int> Size of z-padding to enable deformation at edges when
using SyN. (default: 5)
-x {nn,linear,spline}
Final interpolation. (default: linear)
-ofolder <folder> Output folder. Example: `reg_results`
-qc <folder> The path where the quality control generated content
will be saved. Note: This flag requires the `-dseg`
flag.
-qc-dataset <str> If provided, this string will be mentioned in the QC
report as the dataset the process was run on.
-qc-subject <str> If provided, this string will be mentioned in the QC
report as the subject the process was run on.
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_register_to_template¶
--
Spinal Cord Toolbox (7.0)
sct_register_to_template -h
--
usage: sct_register_to_template -i <file> -s <file> [-s-template-id <int>]
[-l <file>] [-ldisc <file>] [-lspinal <file>]
[-lrootlet <file>] [-ofolder <folder>]
[-t <folder>] [-c {t1,t2,t2s}]
[-ref {template,subject}] [-param <list>]
[-centerline-algo {polyfit,bspline,linear,nurbs}]
[-centerline-smooth <int>] [-qc <folder>]
[-qc-dataset <str>] [-qc-subject <str>] [-h]
[-v <int>] [-profile-time [<file>]]
[-trace-memory [<folder>]] [-r {0,1}]
Register an anatomical image to the spinal cord MRI template (default: PAM50).
The registration process includes three main registration steps:
1. straightening of the image using the spinal cord segmentation (see
sct_straighten_spinalcord for details);
2. vertebral alignment between the image and the template, using labels along
the spine;
3. iterative slice-wise non-linear registration (see sct_register_multimodal
for details)
To register a subject to the template, try the default command:
```
sct_register_to_template -i data.nii.gz -s data_seg.nii.gz -l
data_labels.nii.gz
```
If this default command does not produce satisfactory results, the `-param`
argument should be tweaked according to the tips given here:
https://spinalcordtoolbox.com/user_section/command-line.html#sct-register-
multimodal
The default registration method brings the subject image to the template, which
can be problematic with highly non-isotropic images as it would induce large
interpolation errors during the straightening procedure. Although the default
method is recommended, you may want to register the template to the subject
(instead of the subject to the template) by skipping the straightening
procedure. To do so, use the parameter `-ref subject`. Example below:
```
sct_register_to_template -i data.nii.gz -s data_seg.nii.gz -l
data_labels.nii.gz -ref subject -param
step=1,type=seg,algo=centermassrot,smooth
=0:step=2,type=seg,algo=columnwise,smooth=0,smoothWarpXY=2
```
Vertebral alignment (step 2) consists in aligning the vertebrae between the
subject and the template.
Two types of labels are possible:
- Vertebrae mid-body labels, created at the center of the spinal cord using
the parameter `-l`;
- Posterior edge of the intervertebral discs, using the parameter `-ldisc`.
If only one label is provided, a simple translation will be applied between the
subject label and the template label. No scaling will be performed.
If two labels are provided, a linear transformation (translation + rotation +
superior-inferior linear scaling) will be applied. The strategy here is to
define labels that cover the region of interest. For example, if you are
interested in studying C2 to C6 levels, then provide one label at C2 and another
at C6. However, note that if the two labels are very far apart (e.g. C2 and
T12), there might be a mis-alignment of discs because a subject's intervertebral
discs distance might differ from that of the template.
If more than two labels are used, a non-linear registration will be applied to
align the each intervertebral disc between the subject and the template, as
described in sct_straighten_spinalcord. This the most accurate method, however
it has some serious caveats:
- This feature is not compatible with the parameter `-ref subject`, where only
a rigid registration is performed.
- Due to the non-linear registration in the S-I direction, the warping field
will be cropped above the top label and below the bottom label. Applying
this warping field will result in a strange-looking registered image that
has the same value above the top label and below the bottom label. But if
you are not interested in these regions, you do not need to worry about it.
We recommend starting with 2 labels, then trying the other options on a case-by-
case basis depending on your data.
More information about label creation can be found at
https://spinalcordtoolbox.com/user_section/tutorials/vertebral-labeling.html
MANDATORY ARGUMENTS:
-i <file> Input anatomical image. Example: `anat.nii.gz`
-s <file> Spinal cord segmentation. Example: `anat_seg.nii.gz`
OPTIONAL ARGUMENTS:
-s-template-id <int> Segmentation file ID to use for registration. The ID is
an integer indicated in the file
'template/info_label.txt'. This 'info_label.txt' file
corresponds to the template indicated by the flag `-t`.
By default, the spinal cord segmentation is used (ID=3),
but if available, a different segmentation such as white
matter segmentation could produce better registration
results. (default: 3)
-l <file> One or two labels (preferred) located at the center of
the spinal cord, on the mid-vertebral slice. Example:
`anat_labels.nii.gz`
For more information about label creation, please see: h
ttps://spinalcordtoolbox.com/user_section/tutorials/vert
ebral-labeling.html
-ldisc <file> File containing disc labels. Labels can be located
either at the posterior edge of the intervertebral
discs, or at the orthogonal projection of each disc onto
the spinal cord (e.g.: the file
`xxx_seg_labeled_discs.nii.gz` output by
sct_label_vertebrae)
If you are using more than 2 labels, all discs covering
the region of interest should be provided. E.g., if you
are interested in levels C2 to C7, then you should
provide disc labels 2,3,4,5,6,7. For more information
about label creation, please refer to https://spinalcord
toolbox.com/user_section/tutorials/vertebral-
labeling.html
-lspinal <file> Labels located in the center of the spinal cord, at the
superior-inferior level corresponding to the mid-point
of the spinal level. Example: `anat_labels.nii.gz`
Each label is a single voxel, which value corresponds to
the spinal level (e.g.: 2 for spinal level 2). If you
are using more than 2 labels, all spinal levels covering
the region of interest should be provided (e.g., if you
are interested in levels C2 to C7, then you should
provide spinal level labels 2,3,4,5,6,7)."
-lrootlet <file> Dorsal nerve rootlets segmentation. Example:
`anat_rootlets.nii.gz`
Only labels within the range C2-C8 are supported. If
labels outside this range are provided, they will be
ignored.
Each value corresponds to the spinal level (e.g.: 2 for
spinal level 2). If you are using more than 2 labels,
all spinal levels covering the region of interest should
be provided (e.g., if you are interested in levels C2 to
C7, then you should provide spinal level labels
2,3,4,5,6,7).
By default, the rootlets labels will be used in 2
places:
- step=0: The center of mass of each label will be
used as landmarks for SI-axis slice alignment with
the rootlets of the template.
- step=1: ANTs BSplineSyn adjustment in the SI-axis
using the shape of the rootlets combined with the
image.
If you are customizing the `-param` argument, you can
choose to omit `step=1`, or choose to manually specify
`step=1` yourself. We recommend starting with the
following `step=1` parameters and adjusting as needed:
step=1,type=rootlet,algo=bsplinesyn,metric=CC,iter=6
x6x3,shrink=8x4x2,smooth=0x0x0,slicewise=0,deformati
on=0 x0x1,gradStep=0.1
-ofolder <folder> Output folder.
-t <folder> Path to template (default: /home/docs/checkouts/readthed
ocs.org/user_builds/spinalcordtoolbox/envs/stable/lib/py
thon3.9/site-packages/data/PAM50)
-c {t1,t2,t2s} Contrast to use for registration. (default: t2)
-ref {template,subject}
Reference for registration: template: subject->template,
subject: template->subject. (default: template)
-param <list> Parameters for registration (see
sct_register_multimodal). Default:
step=0
- type=label
- dof=Tx_Ty_Tz_Rx_Ry_Rz_Sz
step=1
- type=imseg
- algo=centermassrot
- metric=MeanSquares
- iter=10
- smooth=0
- gradStep=0.5
- slicewise=0
- smoothWarpXY=2
- pca_eigenratio_th=1.6
step=2
- type=seg
- algo=bsplinesyn
- metric=MeanSquares
- iter=3
- smooth=1
- gradStep=0.5
- slicewise=0
- smoothWarpXY=2
- pca_eigenratio_th=1.6
-centerline-algo {polyfit,bspline,linear,nurbs}
Algorithm for centerline fitting (when straightening the
spinal cord). (default: bspline)
-centerline-smooth <int>
Degree of smoothing for centerline fitting. Only use
with -centerline-algo {bspline, linear}. (default: 20)
-qc <folder> The path where the quality control generated content
will be saved.
-qc-dataset <str> If provided, this string will be mentioned in the QC
report as the dataset the process was run on.
-qc-subject <str> If provided, this string will be mentioned in the QC
report as the subject the process was run on.
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_resample¶
--
Spinal Cord Toolbox (7.0)
sct_resample -h
--
usage: sct_resample -i <file> [-f <str>] [-mm <str>] [-vox <str>] [-ref <file>]
[-x {nn,linear,spline}] [-o <file>] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
Anisotropic resampling of 3D or 4D data.
MANDATORY ARGUMENTS:
-i <file> Image to resample. Can be 3D or 4D. (Cannot be 2D)
Example: `dwi.nii.gz`
METHOD TO SPECIFY NEW SIZE:
Please choose only one of the 4 options:
-f <str> Resampling factor in each dimensions (x,y,z). Separate
with `x`. Example: `0.5x0.5x1`
For 2x upsampling, set to `2`. For 2x downsampling set
to `0.5`
-mm <str> New resolution in mm. Separate dimension with `x`.
Example: `0.1x0.1x5`
Note: Resampling can only approximate a desired `mm`
resolution, given the limitations of discrete voxel data
arrays.
-vox <str> Resampling size in number of voxels in each dimensions
(x,y,z). Separate with `x`.
-ref <file> Reference image to resample input image to. The voxel
dimensions and affine of the reference image will be
used.
OPTIONAL ARGUMENTS:
-x {nn,linear,spline}
Interpolation method. (default: linear)
-o <file> Output file name. Example: `dwi_resampled.nii.gz`
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_run_batch¶
--
Spinal Cord Toolbox (7.0)
sct_run_batch -h
--
usage: sct_run_batch [-config CONFIG] [-jobs <int>] [-itk-threads <int>]
[-path-data PATH_DATA] [-subject-prefix SUBJECT_PREFIX]
[-path-output PATH_OUTPUT] [-batch-log BATCH_LOG]
[-include INCLUDE]
[-include-list INCLUDE_LIST [INCLUDE_LIST ...]]
[-exclude EXCLUDE]
[-exclude-list EXCLUDE_LIST [EXCLUDE_LIST ...]]
[-ignore-ses] [-path-segmanual PATH_SEGMANUAL]
[-script-args SCRIPT_ARGS] [-email-to EMAIL_TO]
[-email-from EMAIL_FROM] [-email-host EMAIL_HOST]
[-continue-on-error {0,1}] [-script SCRIPT] [-zip]
[-v <int>] [-h]
Wrapper to processing scripts, which loops across subjects. Subjects should be
organized as folders within a single directory. We recommend following the BIDS
convention (https://bids.neuroimaging.io/). The processing script should accept
a subject directory as its only argument. Additional information is passed via
environment variables and the arguments passed via `-script-args`. If the script
or the input data are located within a git repository, the git commit is
displayed. If the script or data have changed since the latest commit, the
symbol "*" is added after the git commit number. If no git repository is found,
the git commit version displays "?!?". The script is copied on the output folder
(`-path-out`).
optional arguments:
-config CONFIG, -c CONFIG
A json (`.json`) or yaml (`.yml`/`.yaml`) file with
arguments. All arguments to the configuration file are
the same as the command line arguments, except all
dashes (`-`) are replaced with underscores (`_`). Using
command line flags can be used to override arguments
provided in the configuration file, but this is
discouraged. Please note that while quotes are optional
for strings in YAML omitting them may cause parse
errors.
Note that for the `"exclude_list"` (or `"include_list"`)
argument you can exclude/include entire subjects or
individual sessions; see examples below.
Example YAML configuration:
```
path_data : "~/sct_data"
path_output : "~/pipeline_results"
script : "nature_paper_analysis.sh"
jobs : -1
exclude_list : ["sub-01/ses-01", "sub-02", "ses-03"]
# this will exclude ses-01 for sub-01, all sessions
for sub-02 and ses-03 for all subjects
```
Example JSON configuration:
```
{
"path_data" : "~/sct_data",
"path_output" : "~/pipeline_results",
"script" : "nature_paper_analysis.sh",
"jobs" : -1,
"exclude_list" : ["sub-01/ses-01", "sub-02",
"ses-03"]
}
```
-jobs <int> The number of jobs to run in parallel. Either an integer
greater than or equal to one specifying the number of
cores, 0 or a negative integer specifying number of
cores minus that number. For example `-jobs -1` will run
with all the available cores minus one job in parallel.
Set `-jobs 0` to use all available cores.
This argument enables process-based parallelism, while
`-itk-threads` enables thread-based parallelism. You may
need to tweak both to find a balance that works best for
your system. (default: 1)
-itk-threads <int> Sets the environment variable
`ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS`.
Number of threads to use for ITK based programs
including ANTs. Increasing this can provide a
performance boost for high-performance (multi-core)
computing environments. However, increasing the number
of threads may also result in a large increase in
memory.
This argument enables thread-based parallelism, while
`-jobs` enables process-based parallelism. You may need
to tweak both to find a balance that works best for your
system. (default: 1)
-path-data PATH_DATA Setting for environment variable: `PATH_DATA`
Path containing subject directories in a consistent
format)
-subject-prefix SUBJECT_PREFIX
Subject prefix, defaults to "sub-" which is the prefix
used for BIDS directories. If the subject directories do
not share a common prefix, an empty string can be passed
here. (default: sub-)
-path-output PATH_OUTPUT
Base directory for environment variables:
- `PATH_DATA_PROCESSED=<path-output>/data_processed`
- `PATH_RESULTS=<path-output>/results`
- `PATH_QC=<path-output>/qc`
- `PATH_LOG=<path-output>/log`
Which are respectively output paths for the processed
data, results, quality control (QC) and logs (default:
.)
-batch-log BATCH_LOG A log file for all terminal output produced by this
script (not necessarily including the individual job
outputs. File will be relative to "<path-output>/log".
(default: sct_run_batch_log.txt)
-include INCLUDE Optional regex used to filter the list of subject
directories. Only process a subject if they match the
regex. Inclusions are processed before exclusions.
Cannot be used with `include-list`.
-include-list INCLUDE_LIST [INCLUDE_LIST ...]
Optional space separated list of subjects or sessions to
include. Only process subjects or sessions if they are
on this list. Inclusions are processed before
exclusions. Cannot be used with `-include`. You can
combine subjects and sessions; see examples.
Examples: `-include-list sub-001 sub-002` or `-include-
list sub-001/ses-01 ses-02`
-exclude EXCLUDE Optional regex used to filter the list of subject
directories. Only process a subject if they do not match
the regex. Exclusions are processed after inclusions.
Cannot be used with `exclude-list`
-exclude-list EXCLUDE_LIST [EXCLUDE_LIST ...]
Optional space separated list of subjects or sessions to
exclude. Only process subjects or sessions if they are
not on this list. Inclusions are processed before
exclusions. Cannot be used with `-exclude`. You can
combine subjects and sessions; see examples.
Examples: `-exclude-list sub-003 sub-004` or `-exclude-
list sub-003/ses-01 ses-02`
-ignore-ses By default, if 'ses' subfolders are present, then
'sct_run_batch' will run the script within each
individual 'ses' subfolder. Passing `-ignore-ses` will
change the behavior so that 'sct_run_batch' will not go
into each 'ses' folder. Instead, it will run the script
on just the top-level subject folders. (default: False)
-path-segmanual PATH_SEGMANUAL
Setting for environment variable: PATH_SEGMANUAL
A path containing manual segmentations to be used by the
script program. (default: .)
-script-args SCRIPT_ARGS
A quoted string with extra arguments to pass to the
script. For example: `sct_run_batch -path-data data/
-script process_data.sh -script-args "ARG1 ARG2"`.
The arguments are retrieved by a script as `${2}`,
`${3}`, etc.
- Note: `${1}` is reserved for the subject folder name,
which is retrieved automatically.
- Note: Do not use `~` in the path. Use `${HOME}`
instead.)
-email-to EMAIL_TO Optional email address where sct_run_batch can send an
alert on completion of the batch processing.
-email-from EMAIL_FROM
Optional alternative email to use to send the email.
Defaults to the same address as `-email-to`
-email-host EMAIL_HOST
Optional smtp server and port to use to send the email.
Defaults to gmail's server. Note that gmail server
requires 'Less secure apps access' to be turned on,
which can be done at
https://myaccount.google.com/security (default:
smtp.gmail.com:587)
-continue-on-error {0,1}
Whether the batch processing should continue if a
subject fails. (default: 1)
-script SCRIPT Shell script used to process the data.
-zip Create zip archive of output folders log/, qc/ and
results/. (default: False)
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode (default:
1)
-h, --help show this help message and exit
sct_smooth_spinalcord¶
--
Spinal Cord Toolbox (7.0)
sct_smooth_spinalcord -h
--
usage: sct_smooth_spinalcord -i <file> -s <file> [-smooth <list>]
[-algo-fitting <str>] [-o <file>] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
[-r {0,1}]
Smooth the spinal cord along its centerline. Steps are:
1. Spinal cord is straightened (using centerline),
2. a Gaussian kernel is applied in the superior-inferior direction,
3. then cord is de-straightened as originally.
MANDATORY ARGUMENTS:
-i <file> Image to smooth. Example: `data.nii.gz`
-s <file> Spinal cord centerline or segmentation. Example:
`data_centerline.nii.gz`
OPTIONAL ARGUMENTS:
-smooth <list> Sigma (standard deviation) of the smoothing Gaussian
kernel (in mm). For isotropic smoothing you only need to
specify a value (e.g. `2`). For anisotropic smoothing
specify a value for each axis, separated with a comma.
The order should follow axes Right-Left, Antero-
Posterior, Superior-Inferior (e.g.: `1,1,3`). For no
smoothing, set value to `0`. (default: [0, 0, 3])
-algo-fitting <str> Algorithm for curve fitting. For more information, see
`sct_straighten_spinalcord`. (default: bspline)
-o <file> Output filename. Example: `smooth_sc.nii.gz`. If not
provided, the suffix `_smooth` will be added to the
input file name.
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_straighten_spinalcord¶
--
Spinal Cord Toolbox (7.0)
sct_straighten_spinalcord -h
--
usage: sct_straighten_spinalcord -i <file> -s <file> [-dest <file>]
[-ldisc-input <file>] [-ldisc-dest <file>]
[-disable-straight2curved]
[-disable-curved2straight]
[-speed-factor <float>] [-xy-size <float>]
[-o <file>] [-ofolder <folder>]
[-centerline-algo {bspline,linear,nurbs}]
[-centerline-smooth <int>] [-param <list>]
[-x {nn,linear,spline}] [-qc <str>]
[-qc-dataset <str>] [-qc-subject <str>] [-h]
[-v <int>] [-profile-time [<file>]]
[-trace-memory [<folder>]] [-r {0,1}]
This program takes as input an anatomic image and the spinal cord centerline (or
segmentation), and returns the an image of a straightened spinal cord.
Reference: De Leener B, Mangeat G, Dupont S, Martin AR, Callot V, Stikov N,
Fehlings MG, Cohen-Adad J. Topologically-preserving straightening of spinal cord
MRI. J Magn Reson Imaging. 2017 Oct;46(4):1209-1219
MANDATORY ARGUMENTS:
-i <file> Input image with curved spinal cord. Example:
`t2.nii.gz`
-s <file> Spinal cord centerline (or segmentation) of the input
image. To obtain the centerline, you can use
sct_get_centerline.
To obtain the segmentation you can use `sct_propseg` or
`sct_deepseg spinalcord`.
Example: `centerline.nii.gz`
OPTIONAL ARGUMENTS:
-dest <file> Spinal cord centerline (or segmentation) of a
destination image (which could be straight or curved).
An algorithm scales the length of the input centerline
to match that of the destination centerline. If using
`-ldisc-input` and `-ldisc-dest` with this parameter,
instead of linear scaling, the source centerline will be
non-linearly matched so that the inter-vertebral discs
of the input image will match that of the destination
image. This feature is particularly useful for
registering to a template while accounting for disc
alignment.
-ldisc-input <file> Labels located at the posterior edge of the
intervertebral discs, for the input image (`-i`). All
disc covering the region of interest should be provided.
Exmaple: if you are interested in levels C2 to C7, then
you should provide disc labels 2,3,4,5,6,7). More
details about label creation at https://spinalcordtoolbo
x.com/user_section/tutorials/vertebral-labeling.html.
This option must be used with the `-ldisc-dest`
parameter.
-ldisc-dest <file> Labels located at the posterior edge of the
intervertebral discs, for the destination file
(`-dest`). The same comments as in `-ldisc-input` apply.
This option must be used with the `-ldisc-input`
parameter.
-disable-straight2curved
Disable straight to curved transformation computation,
in case you do not need the output warping field
straight-->curve (faster). (default: False)
-disable-curved2straight
Disable curved to straight transformation computation,
in case you do not need the output warping field
curve-->straight (faster). (default: False)
-speed-factor <float>
Acceleration factor for the calculation of the
straightening warping field. This speed factor enables
an intermediate resampling to a lower resolution, which
decreases the computational time at the cost of lower
accuracy. A speed factor of 2 means that the input image
will be downsampled by a factor 2 before calculating the
straightening warping field. For example, a 1x1x1 mm^3
image will be downsampled to 2x2x2 mm3, providing a
speed factor of approximately 8. Note that accelerating
the straightening process reduces the precision of the
algorithm, and induces undesirable edges effects.
Default=1 (no downsampling). (default: 1)
-xy-size <float> Size of the output FOV in the RL/AP plane, in mm. The
resolution of the destination image is the same as that
of the source image (`-i`). Default: `35`. (default:
35.0)
-o <file> Straightened file. By default, the suffix "_straight"
will be added to the input file name.
-ofolder <folder> Output folder (all outputs will go there). (default: .)
-centerline-algo {bspline,linear,nurbs}
Algorithm for centerline fitting. Default: nurbs.
(default: nurbs)
-centerline-smooth <int>
Degree of smoothing for centerline fitting. Only use
with -centerline-algo {bspline, linear}. Default: `10`
(default: 10)
-param <list> Parameters for spinal cord straightening. Separate
arguments with ','.
- `precision`: Float `[1, inf)` Precision factor of
straightening, related to the number of slices.
Increasing this parameter increases the precision
along with increased computational time. Not taken
into account with Hanning fitting method. Default=`2`
- `threshold_distance`: Float `[0, inf)` Threshold at
which voxels are not considered into displacement.
Increase this threshold if the image is blackout
around the spinal cord too much. Default=`10`
- `accuracy_results`: `{0, 1}` Disable/Enable
computation of accuracy results after straightening.
Default=`0`
- `template_orientation`: {0, 1}` Disable/Enable
orientation of the straight image to be the same as
the template. Default=`0`
-x {nn,linear,spline}
Final interpolation. Default: `spline`. (default:
spline)
-qc <str> The path where the quality control generated content
will be saved
-qc-dataset <str> If provided, this string will be mentioned in the QC
report as the dataset the process was run on
-qc-subject <str> If provided, this string will be mentioned in the QC
report as the subject the process was run on
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_warp_template¶
--
Spinal Cord Toolbox (7.0)
sct_warp_template -h
--
usage: sct_warp_template -d <file> -w <file> [-a <int>] [-s <int>]
[-ofolder <folder>] [-t <folder>] [-qc <folder>]
[-qc-dataset <str>] [-qc-subject <str>] [-histo <int>]
[-h] [-v <int>] [-profile-time [<file>]]
[-trace-memory [<folder>]]
This function warps the template and all atlases to a destination image.
MANDATORY ARGUMENTS:
-d <file> Destination image the template will be warped to.
Example: `dwi_mean.nii.gz`
-w <file> Warping field. `Example: `warp_template2dmri.nii.gz`
OPTIONAL ARGUMENTS:
-a <int> Warp atlas of white matter. (default: 1)
-s <int> Warp spinal levels. DEPRECATED: As of SCT v6.1,
probabilistic spinal levels have been replaced with a
single integer spinal level file, which can be found
inside of the warped 'template/' folder. The '-s' option
is no longer needed.
For more information on the rationale behind this
decision, please refer to:
- https://github.com/spinalcordtoolbox/PAM50/issues/16
- https://forum.spinalcordmri.org/t/updating-spinal-
levels-feedback-needed/1136
(default: 0)
-ofolder <folder> Name of output folder. (default: label)
-t <folder> Path to template. (default: /home/docs/checkouts/readthe
docs.org/user_builds/spinalcordtoolbox/envs/stable/lib/p
ython3.9/site-packages/data/PAM50)
-qc <folder> The path where the quality control generated content
will be saved.
-qc-dataset <str> If provided, this string will be mentioned in the QC
report as the dataset the process was run on.
-qc-subject <str> If provided, this string will be mentioned in the QC
report as the subject the process was run on.
-histo <int> Warp histology atlas from Duval et al. Neuroimage 2019
(https://pubmed.ncbi.nlm.nih.gov/30326296/). (default:
0)
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
System Commands¶
sct_check_dependencies¶
--
Spinal Cord Toolbox (7.0)
sct_check_dependencies -h
--
usage: sct_check_dependencies [-complete] [-short] [-h] [-v <int>]
[-profile-time [<file>]]
[-trace-memory [<folder>]]
Check the installation and environment variables of the toolbox and its
dependencies.
OPTIONAL ARGUMENTS:
-complete Complete test. (default: False)
-short Short test. Only shows SCT version, CPU cores and RAM
available. (default: False)
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
sct_version¶
7.0
sct_deepseg_lesion [DEPRECATED]¶
--
Spinal Cord Toolbox (7.0)
sct_deepseg_lesion -h
--
/home/docs/checkouts/readthedocs.org/user_builds/spinalcordtoolbox/envs/stable/lib/python3.9/site-packages/spinalcordtoolbox/scripts/sct_deepseg_lesion.py:87: DeprecationWarning: [31m[1m`sct_deepseg_lesion` is deprecated, and will be removed in a future version of SCT. Please use `sct_deepseg ms_lesion` instead.[0m
warn(
usage: sct_deepseg_lesion -i <file> -c {t2,t2_ax,t2s}
[-centerline {svm,cnn,viewer,file}]
[-file_centerline <str>] [-brain {0,1}]
[-ofolder <str>] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
[-r {0,1}]
MS lesion Segmentation using convolutional networks. Reference: Gros C et al.
Automatic segmentation of the spinal cord and intramedullary multiple sclerosis
lesions with convolutional neural networks. Neuroimage. 2018 Oct 6;184:901-915.
MANDATORY ARGUMENTS:
-i <file> Input image. Example: `t2.nii.gz`
-c {t2,t2_ax,t2s} Type of image contrast.
- `t2`: T2w scan with isotropic or anisotropic
resolution.
- `t2_ax`: T2w scan with axial orientation and thick
slices.
- `t2s`: T2*w scan with axial orientation and thick
slices.
OPTIONAL ARGUMENTS:
-centerline {svm,cnn,viewer,file}
Method used for extracting the centerline:
- `svm`: Automatic detection using Support Vector
Machine algorithm.
- `cnn`: Automatic detection using Convolutional
Neural Network.
- `viewer`: Semi-automatic detection using manual
selection of a few points with an interactive viewer
followed by regularization.
- `file`: Use an existing centerline (use with flag
`-file_centerline`)
(default: svm)
-file_centerline <str>
Input centerline file (to use with flag `-centerline`
file). Example: `t2_centerline_manual.nii.gz`
-brain {0,1} Indicate if the input image contains brain sections (to
speed up segmentation). This flag is only effective with
`-centerline cnn`. (default: 1)
-ofolder <str> Output folder. (default: /home/docs/checkouts/readthedoc
s.org/user_builds/spinalcordtoolbox/checkouts/stable/doc
umentation/source)
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)
sct_deepseg_sc [DEPRECATED]¶
--
Spinal Cord Toolbox (7.0)
sct_deepseg_sc -h
--
/home/docs/checkouts/readthedocs.org/user_builds/spinalcordtoolbox/envs/stable/lib/python3.9/site-packages/spinalcordtoolbox/scripts/sct_deepseg_sc.py:112: DeprecationWarning: [31m[1m`sct_deepseg_sc` is deprecated, and will be removed in a future version of SCT. Please use `sct_deepseg spinalcord` instead.[0m
warn(stylize(
usage: sct_deepseg_sc -i <file> -c {t1,t2,t2s,dwi}
[-centerline {svm,cnn,viewer,file}]
[-file_centerline <str>] [-thr <float>] [-brain {0,1}]
[-kernel {2d,3d}] [-ofolder <str>] [-o <file>] [-qc <str>]
[-qc-dataset <str>] [-qc-subject <str>] [-h] [-v <int>]
[-profile-time [<file>]] [-trace-memory [<folder>]]
[-r {0,1}]
Spinal Cord Segmentation using convolutional networks. Reference: Gros et al.
Automatic segmentation of the spinal cord and intramedullary multiple sclerosis
lesions with convolutional neural networks. Neuroimage. 2019 Jan 1;184:901-915.
MANDATORY ARGUMENTS:
-i <file> Input image. Example: `t1.nii.gz`
-c {t1,t2,t2s,dwi} Type of image contrast.
OPTIONAL ARGUMENTS:
-centerline {svm,cnn,viewer,file}
Method used for extracting the centerline:
- `svm`: Automatic detection using Support Vector
Machine algorithm.
- `cnn`: Automatic detection using Convolutional
Neural Network.
- `viewer`: Semi-automatic detection using manual
selection of a few points with an interactive viewer
followed by regularization.
- `file`: Use an existing centerline (use with flag
`-file_centerline`)
(default: svm)
-file_centerline <str>
Input centerline file (to use with flag `-centerline`
file). Example: `t2_centerline_manual.nii.gz`
-thr <float> Binarization threshold (between `0` and `1`) to apply to
the segmentation prediction. Set to `-1` for no
binarization (i.e. soft segmentation output). The
default threshold is specific to each contrast and was
estimated using an optimization algorithm. More details
at: https://github.com/sct-pipeline/deepseg-threshold.
-brain {0,1} Indicate if the input image contains brain sections (to
speed up segmentation). Only use with `-centerline cnn`.
(default: `1` for T1/T2 contrasts, `0` for T2*/DWI
contrasts)
-kernel {2d,3d} Choice of kernel shape for the CNN. Segmentation with 3D
kernels is slower than with 2D kernels. (default: 2d)
-ofolder <str> Output folder. (default: /home/docs/checkouts/readthedoc
s.org/user_builds/spinalcordtoolbox/checkouts/stable/doc
umentation/source)
-o <file> Output filename. Example: `spinal_seg.nii.gz`
-qc <str> The path where the quality control generated content
will be saved
-qc-dataset <str> If provided, this string will be mentioned in the QC
report as the dataset the process was run on
-qc-subject <str> If provided, this string will be mentioned in the QC
report as the subject the process was run on
MISC ARGUMENTS:
-h, --help Show this help message and exit.
-v <int> Verbosity. 0: Display only errors/warnings, 1:
Errors/warnings + info messages, 2: Debug mode.
(default: 1)
-profile-time [<file>]
Enables time-based profiling of the program, dumping the
results to the specified file.
If no file is specified, human-readable results are
placed into a 'time_profiling_results.txt' document in
the current directory ('/home/docs/checkouts/readthedocs
.org/user_builds/spinalcordtoolbox/checkouts/stable/docu
mentation/source'). If the specified file is a `.prof`
file, the file will instead be in binary format, ready
for use with common post-profiler utilities (such as
`snakeviz`).
-trace-memory [<folder>]
Enables memory tracing of the program.
When active, a measure of the peak memory (in KiB) will
be output to the file `peak_memory.txt`. Optionally,
developers can also modify the SCT code to add
additional `snapshot_memory()` calls. These calls will
'snapshot' the memory usage at that moment, saving the
memory trace at that point into a second file
(`memory_snapshots.txt`).
By default, both outputs will be placed in the current
directory ('/home/docs/checkouts/readthedocs.org/user_bu
ilds/spinalcordtoolbox/checkouts/stable/documentation/so
urce'). Optionally, you may provide an alternative
directory (`-trace-memory <dir_name>`), in which case
all files will be placed in that directory instead.
Note that this WILL incur an overhead to runtime, so it
is generally advised that you do not run this in
conjunction with the time profiler or in time-sensitive
contexts.
-r {0,1} Remove temporary files. (default: 1)