External Email - Use Caution Hello Freesurfer user, I am very much new to the use of freesurfer. Can anyone share from where to study so that I can start using freesurfer. I basically wants to extract hippocampus trophies and GM WM CSF volumes
Regards: Rahul Sharma +91-9827834360 *"Manners Maketh Man"* On Fri, Jun 12, 2020 at 8:06 PM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > 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 < > franziska.kl...@uni-oldenburg.de> 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: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Douglas N. Greve < > dgr...@mgh.harvard.edu> > >> Gesendet: Montag, 8. Juni 2020 16:23:12 > >> An: freesurfer@nmr.mgh.harvard.edu > >> 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: freesurfer@nmr.mgh.harvard.edu<mailto: > freesurfer@nmr.mgh.harvard.edu> > >> 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 > >> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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