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.klein@uni-oldenburg.de> wrote:
>>
>>
>>          External Email - Use Caution
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>> 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).
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>>
>> 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.
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>>
>> Any thoughts about this are very welcome.
>>
>>
>> Thanks,
>>
>> Franziska
>>
>>
>>
>>
>> ________________________________
>> Von: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> im Auftrag von Douglas N. Greve <dgreve@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
>>
>>
>>
>>
>>
>>
>>
>>
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