sct_qc

Generate Quality Control (QC) report following SCT processing.

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}] [-custom-labels JSON] [-qc QC]
              [-qc-dataset DATASET] [-qc-subject SUBJECT] [-fps float] [-h]
              [-v <int>]

MANDATORY ARGUMENTS

-i

Input image #1

-p

Possible choices: 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

Input segmentation or label

-d

Input image #2 to overlay on image #1 (requires a segmentation), or output of another process. Example: sct_straighten_spinalcord

-plane

Possible choices: axial, sagittal

Plane of the output QC. Only relevant for -p sct_deepseg_lesion.

-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

Possible choices: 0, 1

If set to 0, text won’t be drawn on top of labels. Only relevant for -p sct_label_vertebrae.

Default: 1

-custom-labels

Path to a JSON file containing custom region labels. Only relevant for -p sct_label_vertebrae.

Default: '/home/docs/checkouts/readthedocs.org/user_builds/spinalcordtoolbox/checkouts/5197/spinalcordtoolbox/reports/sct_label_vertebrae_regions.json'

-qc

Path to save QC report.

Default: './qc'

-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

-fps

The number of frames per second for output gif images. Only useful for sct_fmri_moco and sct_dmri_moco.

Default: 5

MISC ARGUMENTS

-v

Possible choices: 0, 1, 2

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

Default: 1

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