Segmentation tutorials
GUI
After opening the HippMapper GUI, click “Hippocampus” under the “Segmentation” tab. Wait for a new pop-up window to appear. The window should look like the image below.
Click “Select t1w” and chose your T1 image. Click “Run”. Type your desired output name in the “out” box. Your output file will automatically appear in your t1w folder.
Command Line
hippmapper seg_hipp
Optional arguments:
-s , --subj input subject
-t1 , --t1w input T1-weighted
-b, --bias bias field correct image before segmentation
-o , --out output prediction
-f, --force overwrite existing segmentation
-ss , --session input session for longitudinal studies
Examples:
hippmapper seg_hipp -s subjectname -b
hippmapper seg_hipp -t1 subject_T1_nu.nii.gz -o subject_hipp.nii.gz
The output should look like this.: