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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Colm Connolly
October 01, 2014 04:37PM
Hi everybody,

I wonder of any one can tell me if there is any way to provide non-Freesurfer derived GM and WM masks (in my case generated by FSL's FAST) to afni_restproc.py ?

From reading the help and code for afni_restproc.py the answer seems to be a no, which leaves me with two options

1. patch the afni_restproc.py code to accept separate masks for GM and WM masks and process them in a manner similar to aseg.

2. Run afni_restproc.py with an aseg provided and then patch the resultant script to use my FAST masks, then pass the patched script through sed to make it work with other subjects.

Are there other options that I'm missing?

Thanks,

Colm.
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afni_restproc.py and non-Freesurfer GM and WM masks

Colm Connolly October 01, 2014 04:37PM

Re: afni_restproc.py and non-Freesurfer GM and WM masks

rick reynolds October 01, 2014 09:35PM