Thank you so much for your help Paul! I was wondering if I could get a little
more specific help with the .ctab file. Would I just add my ROI to the existing
FreesurferColorLUT.txt (named something different of course) or would I start a
new one from scratch?
Thanks again!
Tara
----- Original Message -----
From: "Paul Beach" <pabea...@gmail.com>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>, misko...@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 < misko...@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 )
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