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