Thank you for forwarding this. 

I realize I need to further clarify my issue as well. 

With the help of Doug Greve I've taken hand made ROIs in tksurfer, repackaged them into a new annotation, and repackaged that into a new aseg file for an average subject. Now (and this is where I'm stuck) I'm trying to take those newly minted ROIs, place them onto individual subjects' brains and THEN send them to Afni for each of those subjects (before doing seed correlation analysis).

Previously I had been using mri_label2label to place the averaged subject ROI into single subjects' folders and then mri_label2vol to get them ready to send to Afni. However, this method was not producing ROIs that covered the extent of a region's gray matter. Thus, Doug's solution of re-annotating and re-segmenting. 

Hopefully that makes things a bit easier.


Thanks again for your help!
Paul


On Mon, Feb 18, 2013 at 3:13 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Paul

we usually call those labels and have an ascii label file format. Not sure how to get that into AFNI, but I'm zure Ziad (ccd) knows.

cheers
Bruce

On Mon, 18 Feb 2013, Paul Beach wrote:

Hi there,
Through the help of the Freesurfer Q&A staff I've been able to get ROIs
drawn in tksurfer into an augmented aparc+aseg file of an averaged subject.
I need to be able to get those ROIs, which are not part of the color LUT,
into Afni space.

For ROIs that are already in the LUT, getting them to Afni is no problem, I
simply use a 3dcalc command. However, I have the problem of needing to
export newly parcellated and segmented ROIs that aren't in the Freesurfer
LUT to Afni space. 

Is there a way to do this short of creating a new "spot" for them in our
LUT? If not, how does one go about adding ROIs to the LUT and/or creating a
LUT specific to my needs (since the Wiki suggests not fussing with the
original LUT)?


Thanks,
Paul
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Paul Beach
DO/PhD candidate - Year V
Michigan State University
- College of Osteopathic Medicine - OMS V
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology
- President: American Physician Scientist Association, MSU COM Chapter