Command line usage - Defacing¶
visualqc_defacing: rate quality of defaced MR scan.
usage: visualqc_defacing [-h] [-u USER_DIR] [-d DEFACED_NAME] [-m MRI_NAME] [-r RENDER_NAME] [-o OUT_DIR] [-i ID_LIST] [-so]
Input and output¶
| -u, --user_dir | Absolute path to an input folder containing defaced MRI scans.
Each subject will be queried after its ID ,
and is expected to have the MRI (specified E.g. |
| -d, --defaced_name | |
Specifies the name of defaced MRI image to be rated. Default: defaced.nii | |
| -m, --mri_name | Specifies the name of MRI image that is NOT defaced, to check the accuracy of the defacing algorithm. Default: orig.mgz |
| -r, --render_name | |
Specifies the name of 3D render of the MRI scan. Default: render.png | |
| -o, --out_dir | Output folder to store the visualizations & ratings.
Default: a new folder called visualqc will be created inside the input folder |
| -i, --id_list | Absolute path to file containing list of subject IDs to be processed. If not provided, all the subjects with required files will be processed. E.g. sub001
sub002
cn_003
cn_004
|
| -so, --screenshot_only | |
| This flag enables the batch generation of screenshots of the visualizations generated, for archival purposes. This would skip the interactive and deeper review of the visualizations, and directly saves the screenshots to the output folder. Hence, only some static options would work, and dynamic animations would not. This is NOT recommended as a QC procedure as the generated screenshots can become out of sync with the actual data for a number of reasons, and for reliable and accurate QC, we recommend interactive review which presents fresh visualizations based on latest version of data on disk. | |