Pulling a skull from MR

[BDhoth (Becky Dickinson)]

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 (Andras Lasso)]

I woild recommend the HDBrainExtraction extension for skull stripping. See some more details in this recent discussion:

Brain Segmentation in MR

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 (Becky Dickinson)]

I use the HD brain extraction to get a brain segmentation, but this can be used to KEEP only the skull??
Thank you!

[lassoan (Andras Lasso)]

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 (Becky Dickinson)]

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

[nadayoda59 (daniel)]

Have you solved this problem? If you have, please share your method. Thank you.

[BDhoth (Becky Dickinson)]

No, I have not in a simple way besides going almost slice by slice and interpolating the slices.