AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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Levon
January 10, 2017 02:12PM
Hello AFNI community,

I am having trouble applying AFNI's 3dSkullStrip to the anatomical data from the Consortium for Neuropsychiatric Phenomics (CNP) dataset (https://openfmri.org/dataset/ds000030/). Specifically, 3dSkullStrip is consistently overstripping the top of the brain (e.g. regions near the left postcentral gyrus) but otherwise performing well on the rest of the brain.

I have tried many of the recommended approaches in the documentation for 3dSkullStrip, including first running 3dUnifize then trying the following options:
-push_to_edge
-shrink_fac
-blur_fwhm
-ld

In general, the above options result in too liberal an expansion of the brain region, capturing too much skull in addition to the problem regions at the top of the brain. Ideally, I would want to only change the brain expansion near the top of the brain only and not change it anywhere else.

Any help would be greatly appreciated.

- Levon Demirdjian
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3dSkullStrip over-stripping top of brain

Levon January 10, 2017 02:12PM