Hi Daniel,
have you run recon-all on your subjects? If so, you can run
mri_annotation2label to convert the ?h.aparc.annot file into separate
labels for each ROI, then go from there. Or if you want to do everything in
average space you can run it on fsaverage (or load the annotation in
tksurfer, click on the one you want and save it as a label instead of
converting every parcel to a label)
cheers
Bruce
On Wed, 19 Jun 2013, Yang, Daniel
wrote:
Hi FreeSurfer expert,
I am interested in a particular region of the Desikan-Killiany atlas and I'd
like to use it as an ROI image mask in my fMRI analysis.
Could you please suggest how I can do that?
From here (http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation), I
see that the DK atlas files are located here:
$FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs
Question 1: how can I read this GCS file?
Question 2: After I read this GCS file, how can I create an ROI image mask?
I am thinking to use the WFU PickAtlas to create an ROI
(http://fmri.wfubmc.edu/software/PickAtlas). Would it be a good fit?
Thanks!
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
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