Hi Inês
nibabel should be able to read freesurfer images directly (thanks to Satra!
I think):
http://nipy.org/nibabel/reference/nibabel.freesurfer.html
cheers
Bruce
On Tue, 20 Nov
2018, Borges Pereira Ines Isabel 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
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