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}] [-qc QC] [-qc-dataset DATASET]
[-qc-subject SUBJECT] [-fps float] [-v] [-h]
Named Arguments¶
- -i
Input image #1 (mandatory)
- -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
- -s
Input segmentation or label
- -d
Input image #2 to overlay on image #1 (requires a segmentation), or output of another process (e.g., 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
- -qc
Path to save QC report. Default:
./qc
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.
- -v
Verbose
Default: False
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