Also, verify that they are shifted (or not) in freeview On 6/10/2020 8:39 AM, Tim Schäfer wrote: > External Email - Use Caution > > Without the code used to plot it's hard to tell why they are not aligned, but > my guess would be that are misaligned by exactly 1 voxel (=mm) as a > consequence of the index shift (0-based indices in C/freesurfer files, > 1-based indices in Matlab). > > Tim > >> On June 10, 2020 at 11:53 AM Franziska Klein >> <[email protected]> wrote: >> >> >> External Email - Use Caution >> >> Hello again! >> >> >> I plotted the meshes of the pialsurface (lh.pial and rh.pial) together with >> the ribbon.mgz and noticed that the ribbon mesh is slightly shifted to the >> right as compared to the pialsurface (see figures attached). >> >> >> I am a little bit confused about this (shouldn't it be aligned?) and was >> wondering which one is the 'correct' one (or how to correct it) in terms of >> the alignment with T1.mgz which I am using in order to perform the >> coregistration (projecting channels onto the head surface). It is really >> important that the brain (ribbon) is correctly located within the head >> because I need to project the channels from the head surface onto the cortex. >> >> >> Any thoughts about this are very welcome. >> >> >> Thanks, >> >> Franziska >> >> >> >> >> ________________________________ >> 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 >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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