Thank you Paul that is very helpful, but I could use a little more specific help.

A little more context: I ran a group vertexwise analysis with all my subjects mapped to the fsaverage and traced my group cluster in QDEC and saved the label. Now I would like to somehow get it into afni in the same space and use it for some functional analyses.

I mapped the label to each individual subjects space, but the next step I am running into issues.

I don't seem to see any medial wall in the aparc annotation. Plus I am not familiar with the color table, I was just wondering what that would look like.

Any help from anyone would be much appreciated!

Tara

----- Original Message -----
From: "Paul Beach" <pabeach1@gmail.com>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>, miskovi2@uwm.edu
Sent: Thursday, June 5, 2014 12:26:00 PM
Subject: Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?


Hi Tara,


I do this regularly, though I don't define my Freesurfer ROIs/labels in QDEC.


The following will do the process into individual subject space


First :
mri_label2label --srclabel path_to_label/label.label --trgsubject {$subj} --regmethod surface --hemi hemisphere


Do this for as many labels as you have...


Then :
Create a color table file (.ctab file) for each hemisphere that contains your ROIs. Take a look at the FreesurferColorLUT.txt file for help with that. The first entry should be the Freesurfer defined medial wall, which you can get from each subject's aparc.annot via mri_annotation2label.


Then create an annotation file using your .ctab file and your ROIs - one for each hemisphere


mris_label2annot --s {$subj} --ldir-default --h hemisphere --ctab hemisphere.ctab_file_name.txt --annot name_for_your_annotation_file \

--l hemi.FS_medial_wall.label \

--l hemi.ROI1.label \
--l hemi.ROI2.label \

--l hemi.ROI3.label \

...


Then create a segmentation file from the annotation file


mri_aparc2aseg --s {$subj} --annot annotion_you_created_without_hemi_designation --o segmentation_file_name+aseg.mgz



Then make a gmroi_vol file from which you can extract your ROIs



mri_label2vol --seg segmentation_file_name+aseg.mgz --regheader segmentation_file_name+aseg.mgz --o you_gmroi_volume.nii.gz --temp orig/001.mgz


Copy the gmroi_vol to your subject's afni directory


Use 3dcalc to extract individual ROIs from the gmroi_volume. The number you put in depends on your .ctab file order. The first ROI would be 1001. Like the ColorLUT, the first digit being '1' is typically for L. hemi, while '2' would be for the R. hemi.


3dcalc -a your_gmroi_volume.nii.gz -expr 'equals(a,####)' -prefix ROI_name.nii.gz





You can then do your AFNI-based analyses with your ROIs.


Hopefully that's all clear. Let me know if I can help in another way.




Cheers,
Paul





On Thu, Jun 5, 2014 at 12:13 PM, Tara Ann Miskovich < miskovi2@uwm.edu > wrote:


Hi all,

I am wondering if any one has any experience with converting a freesurfer surface based ROI created in QDEC into a format I could use on functional data in afni.

Thank you,

Tara

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--

Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU Co gnitive and Ge riatric N eurology T eam ( CoGeNT )