External Email - Use Caution
Dear FreeSurfer experts,
Is it possible using the FS tools to create a grey-white matter boundary binary mask in volume space (e.g., a nifti file) that will be a single voxel thick along the entire grey-white matter boundary?
Many thanks, Tamir
Dr Tamir Eisenstein, Ph.D.
Postdoctoral Researcher
FMRIB, Wellcome Centre for Integrative Neuroimaging
Nuffield Department of Clinical Neurosciences
John Radcliffe Hospital, Oxford OX3 9DU
University of Oxford
tamir.eisenstein@ndcn.ox.ac.ukmailto:julien.fars@ndcn.ox.ac.uk
eisentamir@gmail.commailto:julien.fars@gmail.com
tel: +44 7938790763
You can use mri_surf2vol with the --mkmask option (method 2; see mri_surf2vol --help), eg, cd subject/surf mri_surf2vol --mkmask --hemi lh --o mask.lh.mgz --identity subject --template ../mri/nu.mgz If you want to go to another volume, supply the registration to that volume with --reg instead of using --identity
On 12/16/2024 5:13 AM, Tamir Eisenstein wrote:
External Email - Use Caution
Dear FreeSurfer experts,
Is it possible using the FS tools to create a grey-white matter boundary binary mask in volume space (e.g., a nifti file) that will be a single voxel thick along the entire grey-white matter boundary?
Many thanks, Tamir
*Dr Tamir Eisenstein, Ph.D.*
*Postdoctoral Researcher*
FMRIB, Wellcome Centre for Integrative Neuroimaging
Nuffield Department of Clinical Neurosciences
John Radcliffe Hospital, Oxford OX3 9DU
University of Oxford
tamir.eisenstein@ndcn.ox.ac.uk mailto:julien.fars@ndcn.ox.ac.uk
_eisentamir@gmail.com mailto:julien.fars@gmail.com_
tel: +44 7938790763
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Tamir
I guess a quick and dirty way to do it would be to use mris_expand to create a surface 1mm out from the white, then fill that with mris_ribbon (or maybe mris_fill?). That would probably leave small holes. An alternative would be to use some kind of non-maximum suppression, but I'm not sure we have anything out of the box. I guess it depends on what the properties of the boundary are that are important to you. cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Tamir Eisenstein Sent: Monday, December 16, 2024 5:13 AM To: Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Single voxel grey-white matter boundary binary mask
External Email - Use Caution Dear FreeSurfer experts,
Is it possible using the FS tools to create a grey-white matter boundary binary mask in volume space (e.g., a nifti file) that will be a single voxel thick along the entire grey-white matter boundary?
Many thanks, Tamir
Dr Tamir Eisenstein, Ph.D.
Postdoctoral Researcher
FMRIB, Wellcome Centre for Integrative Neuroimaging
Nuffield Department of Clinical Neurosciences
John Radcliffe Hospital, Oxford OX3 9DU
University of Oxford tamir.eisenstein@ndcn.ox.ac.ukmailto:julien.fars@ndcn.ox.ac.uk
eisentamir@gmail.commailto:julien.fars@gmail.com
tel: +44 7938790763
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Fischl, Bruce R.,PHD -
Tamir Eisenstein