sct_straighten_spinalcord

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

usage: sct_straighten_spinalcord -i <file> -s <file> [-h] [-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>]
                                 [-r {0,1}] [-v <int>]

MANDATORY ARGUMENTS

-i

Input image with curved spinal cord. Example: t2.nii.gz

-s

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_sc. Example: centerline.nii.gz

OPTIONAL ARGUMENTS

-dest

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

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://spinalcordtoolbox.com/user_section/tutorials/vertebral-labeling.html. This option must be used with the -ldisc-dest parameter.

-ldisc-dest

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

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

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

Straightened file. By default, the suffix “_straight” will be added to the input file name.

Default: “”

-ofolder

Output folder (all outputs will go there).

Default: “.”

-centerline-algo

Possible choices: bspline, linear, nurbs

Algorithm for centerline fitting. Default: nurbs.

Default: “nurbs”

-centerline-smooth

Degree of smoothing for centerline fitting. Only use with -centerline-algo {bspline, linear}. Default: 10

Default: 10

-param

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

Possible choices: nn, linear, spline

Final interpolation. Default: spline.

Default: “spline”

-qc

The path where the quality control generated content will be saved

-qc-dataset

If provided, this string will be mentioned in the QC report as the dataset the process was run on

-qc-subject

If provided, this string will be mentioned in the QC report as the subject the process was run on

-r

Possible choices: 0, 1

Remove temporary files.

Default: 1

-v

Possible choices: 0, 1, 2

Verbosity. 0: Display only errors/warnings, 1: Errors/warnings + info messages, 2: Debug mode

Default: 1