Hi Bruce,
That works to some extent, but not exactly as I expected. If I go into the directory of the subject I'm interested and enter:
mri_ribbon ./surf/rh.white ./surf/rh.pial ./mri/orig.mgz rh.ribbon.nii.gz
I get a mask where the white matter is marked by 0, and everything else, both grey matter and outside the brain, are marked by 255. I need to be able to get labels for both white and grey matter, and it would be nice if I could easily create a volume that contained masks for both hemispheres. Ideally, I'd like to be able to run the equivalent of:
mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon bert
but without having an aseg file for bert.
I think I may have found a workaround for my case, but it seems to have a few quirks. Assuming that the aseg.mgz file is mostly used as a reference for volume size, I made a copy of orig.mgz and renamed it aseg.mgz. I then ran mris_volmask with the options listed above. It output the desired labels, with 2 small caveats. First, the data was collected in with the animal in sphinx position, and even though orig.mgz was already corrected for this, the resulting ribbon.mgz file needed to be de-sphinxed. Second, the white matter labeled by this method is expanded relative to the white matter labeled by mri_ribbon. That is to say, the voxels labeled by mris_volmask as white (after de-sphinxing) are the voxels labeled by mri_ribbon, as well as a an additional one voxel border surrounding these voxels. Is this to be expected? Do you think this workaround yields kosher results, and if not, is there a better way to be using mri_ribbon?
Thanks once more, Clark
On Feb 6, 2012, at 8:58 AM, Bruce Fischl wrote:
Hi Clark
I think you can just call mri_ribbon directly using say the orig.mgz as the input_volume_pref.
cheers Bruce On Mon, 6 Feb 2012, Clark Fisher wrote:
Hello,
I'm working with primate data, and I'm wondering: is there any way to create a ribbon.mgz file from surfaces since I don't have aseg.mgz? I can't seem to run mris_volmask without it, and running reconall -autorecon3 -noaseg did not output ribbon.mgz.
Thanks for the help, Clark _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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