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.