sct_warp_template

This function warps the template and all atlases to a destination image.

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>]]

MANDATORY ARGUMENTS

-d

Destination image the template will be warped to. Example: dwi_mean.nii.gz

-w

Warping field. Example: warp_template2dmri.nii.gz`

OPTIONAL ARGUMENTS

-a

Possible choices: 0, 1

Warp atlas of white matter.

Default: 1

-s

Possible choices: 0, 1

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

Name of output folder.

Default: “label”

-t

Path to template.

Default: “/home/docs/checkouts/readthedocs.org/user_builds/spinalcordtoolbox/checkouts/7.0/data/PAM50”

-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.

-histo

Possible choices: 0, 1

Warp histology atlas from Duval et al. Neuroimage 2019 (https://pubmed.ncbi.nlm.nih.gov/30326296/).

Default: 0

MISC ARGUMENTS

-v

Possible choices: 0, 1, 2

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

Default: 1

-profile-time

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/7.0/documentation/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

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_builds/spinalcordtoolbox/checkouts/7.0/documentation/source’). 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.