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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Ziad
January 18, 2012 06:34PM
Hi YIYU,

It depends on what you are trying to do. The easiest thing would be to first run:
@SUMA_Make_Spec_FS -sid SUBJ
in the directory where freesurfer's output for subject SUBJ resides.

The output of this script is a directory called SUMA/ which contains the parcellation volumes in addition to surfaces and assorted data that are transformed to work well with AFNI and SUMA.

In the SUMA directory, you'll end up with files such as:
SUBJ_SurfVol+orig.HEAD
and
aparc.a2009s+aseg_rank.nii which contains a ranked version of the parcellation file all while preserving the labels of the original parcellation volume. Actually AFNI treats that _rank file as an atlas, so you can use whereami to extract ROIs by name.

Give me some more detail about what you want to do and I can be more specific.

cheers,
ziad
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Subject Author Posted

colormap for freesurfer labels

YIYU January 17, 2012 11:08AM

Re: colormap for freesurfer labels

Ziad January 18, 2012 06:34PM