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

History of AFNI updates  

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May 15, 2017 02:12PM
I published something about this a bit ago:
[www.ncbi.nlm.nih.gov]

Essentially what we do is:
1) Trim to 0-100 HU.
2) Smooth the image a bit (1mm^3 gaussian) - not always necessary, but good idea depending on the convolution filter used on the CT (aka bone scans)
3) Run Brain extraction tool (BET) with fractional intensity threshold to 0.01 - 3dSkullStrip implements a modified version of this (I believe this is shrink_fac in 3dSkullStrip)
4) Fill some holes

Here's example FSL bash code:
[github.com]
Subject Author Posted

Skull stripping CT

tpieters February 09, 2017 10:51AM

Re: Skull stripping CT

Daniel Glen February 09, 2017 06:20PM

Re: Skull stripping CT

muschellij2 May 15, 2017 02:12PM

Re: Skull stripping CT

discoraj February 20, 2017 01:40PM