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
February 15, 2009 09:00PM
Hi Derek,

Look at the help from the command line program 'whereami'. You can get any of the ROIs available in any of the atlases distributed in AFNI. Perhaps one of these would do the trick.
Alternately, you can use FreeSurfer to automatically generate ROIs on a per-subject basis. The process may take a day or two but it is fully automated. Once you create the segemented volumes, AFNI's @SUMA_Make_Spec_FS script will port the segmented volumes for use in AFNI.

Regarding your other question. Afni can read Analyze but that format from hell is incomplete so there is no way to know for sure how it should be displayed. You should be using NIFTI for volume transfer across applications.

Upload the volumes and explain how you expect them to overlap. Perhaps someone can help you out.

Lastly, check out the education material for the talk on volume registration and Talairach transformation. It contains examples on how to extract various atlas-based ROIs in AFNI: [afni.nimh.nih.gov]

cheers,
ziad
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Subject Author Posted

anat masks

derek February 15, 2009 04:02PM

Re: anat masks

Ziad February 15, 2009 09:00PM

Re: anat masks

derek February 19, 2009 05:49PM