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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Bob Cox
February 12, 2016 01:29PM
The method we use is

(1) run 3dSkullStrip to produce a "pure" brain volume

(2) run 3dSeg to produce a classified brain volume:

3dSeg -anat anat.nii -mask AUTO -classes 'CSF ; GM ; WM' -bias_classes 'GM ; WM' -bias_fwhm 25 -mixfrac UNI -main_N 5 -blur_meth BIM

(3) the output from 3dSeg is in a directory called Segsy -- the files in there that contains the classification for each voxel are dataset Classes+tlrc.* -- to compute the gray-only mask, pick out all voxels with value=2

3dcalc -a Classes+tlrc -expr 'equals(a,2)' -prefix maskGM
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Subject Author Posted

How to get template mask for gray matter

maitra February 12, 2016 12:06AM

Re: How to get template mask for gray matter

Bob Cox February 12, 2016 01:29PM

Re: How to get template mask for gray matter

maitra February 12, 2016 02:44PM

Re: How to get template mask for gray matter

Bob Cox February 16, 2016 11:57AM