Thanks Bruce, Sorry for the naiive questions - I'm still pretty green. If I define a label for, say, the head of the left sternocleidomastoid, using tkmedit, could I then generalize that label to the rest of my patient cohort using mri_label2label?

Thanks, Jeff

Hi Jeff

our standard segmentation doesn't include muscle. We did have some prototypes that labeled all cranial muscles but they are not much more than prototypes Bruce

On Wed, 1 May 2013, jwaugh@nmr.mgh.harvard.edu wrote:

...

Hello Freesurfers, I would like to use the muscle ROI in the LUT (number 123). Can anyone tell me which muscles (all cranial? cervical too?) are included? I tried making a subject-specific label using the following command: mri_cor2label --c /cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/mri/aseg.mgz --id 123 --l /cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/label/muscle_${identifier}.label

This yielded the error "Found 0 label voxels", presumably because aseg.mgz is skull-stripped. When I used orig.mgz instead of aseg.mgz in the command line above, the assigned label is a scattering of single voxels throughout the cortex and subcortical white matter. I am guessing that this is because orig.mgz is not registered to the same space as aseg.mgz

is this correct?

Any suggestions for how to use the muscle ROI would be much appreciated.

Thanks, Jeff _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer