ANTS - masking to improve brain extraction
- Paul Macey (admin)
Overview
Open image in ITK-SNAP
Create a rough, partial mask of non-brain regions using snakes automatic segmentation, save
Use CAT12 to remove the masked regions
Save the image with extracted non-brain in the anatomical folder, and move the original image and the ITK-SNAP mask into a subfolder
Re-run (delete the study files in the project folder, or check overwrite to redo everything)
Details
Create partial brain mask
Note: does not need every non-brain area.
Open anatomical
Go to Snake segmentation mode
“Segment 3D” (leave default outlines)
Click in problem area (example shows bright region above brain)
Next
Click Add Bubble at Cursor
Adjust size (needed to reduce size in example)
Next
Press “play” - keep ging until the region fills the area you want. Adjusting the praamaters will make it more or less sensitive.
Finish
Save segmentation (saves to *.nii.gz)
Created masked anatomical
Extract mask (from *.nii.gz to *.nii)
Go to CAT12’s “Manual image (lession) maksing (seelsnapshot)
Select images => anatomical
Select lesion masks => mask
Run (other two can stay at default)
For convenience, rename the file. Instead of the prepended “msk_”, use a suffice “….msk.nii”. This keeps the first part of the filename consistent.
Organize the files
Leave the renamed, masked file in the original coreg folder. Create a subfolder and copy the mask files and unmasked file there. See snapshot
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CAT12
File organization
