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Segmentation tutorials
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GUI
After opening the HyperMapper GUI, click “WMH” under the “Segmentation” tab. Wait for a new pop-up window to appear.
Click “Select t1w” and chose your T1 image.
Type your desired output name in the “out” box. Click “Run”. Your output file will automatically appear in your t1w folder.
Command Line
hypermapper seg_wmh
optional arguments:
-h, --help show this help message and exit
-s , --subj input subject
-fl dir, --flair dir input Flair
-t1 , --t1w input T1-weighted
-m , --mask brain mask
-o , --out output prediction
-ign_ort, --ign_ort ignore orientation if tag is wrong
-n , --num_mc number of Monte Carlo Dropout samples
-th , --thresh threshold
-f, --force overwrite existing segmentation
Examples:
hypermapper seg_wmh -s subjectname -b
hypermapper seg_wmh -t1 subject_T1_nu.nii.gz -fl subject_T1acq_nu_FL.nii.gz -m subject_T1acq_nu_HfB.nii.gz -o subject_wmh_pred.nii.gz
The output should look like this.: