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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