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
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
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer