sct_warp_template¶

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

usage: sct_warp_template -d <file> -w <file> [-h] [-a <int>] [-s <int>]
                         [-ofolder <folder>] [-t <folder>] [-qc <folder>]
                         [-qc-dataset <str>] [-qc-subject <str>] [-v <int>]
                         [-histo <int>]

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/stable/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.

-v

Possible choices: 0, 1, 2

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

Default: 1

-histo

Possible choices: 0, 1

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

Default: 0