If you want to use it as a mask in FSFAST, you can do that at the higher level when you run mri_glmfit. You would then extract the label for fsaverage only and pass it to mri_glmfit with the --label option doug

On 6/19/13 11:22 AM, Bruce Fischl wrote:

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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