Segmentation tutorials


Watch this video tutorial: ALT TEXT

Or follow the steps below:

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

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.: