External Email - Use Caution As you said, you can load FreeSurfer data (both the surface files and volume data) with the respective nibabel functions, i.e., read_geometry and read_morph_data. The ?h.pial and ?h.white files are surface meshes, so read_geometry would apply.
I'm not familiar with nighres, but from your description of what you want to do, it seems that you would need volume data for that. It seems impossible to do volumetric layering based on just a mesh. Tim > On November 20, 2018 at 5:08 PM Borges Pereira Ines Isabel > <in...@student.ethz.ch> wrote: > > > External Email - Use Caution > > Dear FreeSurfer developers, > > I am trying to segment the cortex of my subjects into multiple layers and am > trying several approaches. > I have tried the command "mris_expand -thickness lh.white 0.5 lh.graymid" and > it works perfectly. > I am also interested in trying other approaches from other software packages > and have started to experiment with nighres. > > Is it possible to convert the FreeSurfer surface files (pial and white) to a > nibabel SpatialImage format or another format that can be read by the > nibabel/nighres python library? > I have searched the FreeSurfer documentation but couldn’t find a direct > answer. I also see that nibabel has a freesurfer module and hence I am able > to load the images to a python script. However, when I attempt to use perform > volumetric layering with nighres, it returns a value error, given that the > “input volume must be either a path to a file that Nibabel can load or a > nibabel SpatialImage." > > I will also contact the nighres developers but was wondering if Freesurfer > already takes into account the possible interaction between different > software packages. > > Many thanks! > > Best regards, > > Inês Pereira > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Forschung - Klinische Bildgebung Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters Universitätsklinikum Frankfurt / Haus 93, Raum A 305 Deutschordenstr. 50, 60528 Frankfurt am Main Email: tim.schae...@kgu.de| Tel.: +49 (0)69 6301 85832 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
