Hi
Try opening the aparc+aseg image in fslview and check if it has the medial orbitofrontal with the right label.
Saad.
On 12 Aug 2011, at 01:13, Paula Wu wrote:
> Hello all,
>
> I have been trying to use fslmaths to create ROIs from Freesurfer, and have been successful for Freesurfer labels with low numbers (eg. Putamen, #12) but not for high numbers (eg. medial orbitofrontal cortex, #1014). I get an output with a blank nifti file for the below code. Any suggestions?
>
> foreach subject (CON2001 CON2005 CON2007)
> fslmaths /mnt/hgfs/LinuxShare/subjects4freesurfer/$subject/mri/aparc+aseg.nii -thr 1014 -uthr 1014 /mnt/hgfs/LinuxShare/subjects4freesurfer/$subject/mri/$subject'_Medialorbitofrontal_Left_Freesurfer.nii.gz'
> end
>
> Thanks!
>
> Paula
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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