Example usage - Segmentation

In some use cases, you may want to overlay images from arbitrary locations without any pre-defined structure or hierarchy like Freesurfer. This is possible in visualqc_freesurfer by specifying:

1. path to parent folder of the images using --user_dir or -u option, which contains a separate folder for each subject ID
2. name of the anatomical MRI with --mri_name (or -m) and
3. name of the segmentation with --seg_name (or -g) that is to be overlaid on the MRI.

If you would like to review all the subjects (each with their own folder) in /project/MR_segmentation, whose segmentation(s) are stored in roi_set.nii whose T1/anatomical MRI is stored in mri.nii. The folder hierarchy (within /project/MR_segmentation) might look like this:

.
|-- atlas1
|   |-- mri.nii
|   `-- roi_set.nii
|-- atlas2
|   |-- mri.nii
|   `-- roi_set.nii
|-- sub_01
|   |-- mri.nii
|   `-- roi_set.nii
`-- sub_04
    |-- mri.nii
    `-- roi_set.nii

In that case, you would issue the following command:

visualqc_freesurfer --in_dir /project/MR_segmentation --mri_name mri.nii --seg_name roi_set.nii

This will process the four subjects (atlas1, atlas2, sub_01, sub_04) sequentially, and creates an output directory called visualqc in the input directory specified /project/MR_segmentation, to store the visualizations generated, along with the ratings and notes provided by the user. You can also change the output directory with the -o option. You can also limit the review to a subject of IDs, by using a predefined list by a specifying an id list with --id_list or -i option, containing one ID per line. An example (focusing only on the 2 atlases) could like:

atlas1
atlas2