External Email - Use Caution Yes, I do only need cortex gray matter. Great, then I'll use the ribbon.mgz in order to create a gray matter mesh.
Thank you for your answer! ________________________________ Von: [email protected] <[email protected]> im Auftrag von Douglas N. Greve <[email protected]> Gesendet: Montag, 8. Juni 2020 16:23:12 An: [email protected] Betreff: Re: [Freesurfer] How can I create a grey matter volume in Matlab? When you say "gray matter" do you mean all gray matter or just cortex? If just cortex, then you need to take all the voxels between white and pial surfaces. This is already done in the ribbon.mgz file On 6/8/2020 10:05 AM, Franziska Klein wrote: External Email - Use Caution Hello again, unfortunately, nobody is responding. . Until now I am able to create meshes from the freesurfer output files with the isosurface() and read_surf() functions from a MATLAB based toolbox . However, I still do not know with which combinations of the outputs of recon-all I could create a grey matter only mask. My goal is to get subject specific channel MNI coordinates projected onto the cortex (grey matter). My solution at the moment is to simply use the pial surfaces (rh.pial and lh.pial), however, I am not sure if this is sufficient. Any thoughts or ideas maybe? Thanks, Franziska ________________________________ Von: Franziska Klein Gesendet: Mittwoch, 27. Mai 2020 11:05 An: [email protected]<mailto:[email protected]> Betreff: How can I create a grey matter volume in Matlab? Dear freesurfer user, due to the Covid 19 situation I am working in home office with a windows computer and can not run any freesurfer functions (installing a virtual box is not really an option). For all my subjects I do already have all output files from recon all. In the output, I found a wm.mgz but unfortunately there is no gm.mgz. Is it somehow possible to create a grey matter volume by using the recon all output in combination with Matlab? Thank you and kind regards, Franziska ------------------------------------------ Franziska Klein, M.Sc. Neurocognition and Functional Neurorehabilitation Group Neuropsychology Lab Department of Psychology University of Oldenburg D-26111 Oldenburg Germany Office: A7 0-066 Phone: +49-441-798-4947 Fax: +49-441-798-5522 _______________________________________________ Freesurfer mailing list [email protected]<mailto:[email protected]> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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