Quickstart
After installation, users can quickly run a small example:
1. Download the repository (if not already downloaded) and go to examples script directory
git clone https://github.com/CBICA/MRISnapshot cd MRISnapshot/examples/scripts
2. Run the command for data preparation
mrisnapshot_prep_data -i ../scans -s _T1.nii.gz -d ../output --mask _T1_ICVMASK.nii.gz --olay _T1_ICVMASK.nii.gz --olay2 _T1_BRAINMASK.nii.gz
3. Run the command for report creation
mrisnapshot_create_report -d ../output
Note
Alternatively, instead of steps 2 and 3, users can run the example script provided.
./run_example.sh
4. View the QC report (using your favorite browser)
google-chrome ../output/QCReport/qcreport.html
5. Navigate subjects using PREV and NEXT buttons (or left and right arrows), and annotate them by editing the QC form fields
Note
Users can click on a snapshot to open a larger image. On the larger image, they can click again to remove/add the overlay masks
6. Save the QC annotations using the SAVE REPORT button
Note
Depending on the browser type and configuration, the path and naming of the output .csv file may show differences. For example, the output file may be directly saved to a default download folder.