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Hi David, thanks for much for the tips. I also accidentally found out that reslicing FREESURFER_ROI.nii.gz to structural image space also works!


On Mon, Jan 6, 2014 at 7:42 PM, David Soto <[log in to unmask]> wrote:
hi, something like this works for me

mri_binarize --i  /mri/aparc+aseg.mgz --match NUMBER --o /label/FREESURFER_ROI.nii.gz

fslswapdim /label/FREESURFER_ROI.nii.gz x z -y /label/FREESURFER_ROI.nii.gz_FORFSL.nii.gz

mri_convert -i /label/FREESURFER_ROI.nii.gz -rl /t1/output.mnc -o $sub/label/FREESURFER_ROI.nii.gz_FORFSL.nii.gz

fslmaths /label/FREESURFER_ROI.nii.gz_FORFSL.nii.gz  -bin /label/FREESURFER_ROI.nii.gz_FORFSL.nii.gz

cheers
ds



--
Liang-Tien Hsieh (aka Frank)
Ph.D. Candidate
Department of Psychology & Center for Neuroscience
University of California, Davis