BDhoth
September 12, 2024, 3:45pm
1
Are there any tips for pulling a skull from MRI images? In this sequence the skull is very comparable in the number as other brain matter/soft tissue.
lassoan
September 13, 2024, 3:50am
2
I woild recommend the HDBrainExtraction extension for skull stripping. See some more details in this recent discussion:
It looks like you correctly created a brain mask segmentation in white, and a new skull-stripped volume. The green segment looks like it is from a different segmentation node created from threshold of the image before skull stripping.
If you go back to the data view, you can turn off the node named ‘Segmentation’ with the green head label to see only the brain mask label in white.
BDhoth
September 13, 2024, 5:18pm
3
I use the HD brain extraction to get a brain segmentation, but this can be used to KEEP only the skull??
lassoan
September 13, 2024, 6:51pm
4
Yes, sure, you can blank out the brain region by a few clicks.
Create Brain segmentation output in HD Brain Extraction Tool module
Go to Segment Editor module
Click Mask volume effect, Fill inside, and Apply
BDhoth
October 4, 2024, 12:24pm
5
I tried this option, but it doesn’t work the best for getting only the skull. When thresholding it merges right with how it was masked. ANy other options to get a skull only, no soft tissue? Thank you for your help!
Becky
Have you solved this problem? If you have, please share your method. Thank you.
BDhoth
January 3, 2025, 1:04pm
7
No, I have not in a simple way besides going almost slice by slice and interpolating the slices.
jonel
November 11, 2025, 8:31pm
8
If you are still searching for a solution to this problem you might be interested in the new ModalityConverter extension: New extension: ModalityConverter - bringing AI medical image-to-image translation to 3D Slicer You can use it to generate a synthetic CT from your MRI images, from which you can then easily extract the skull with the Segment Editor.
Yes, and here you can also find a video tutorial on how to do it!
