Yes, I agree. Going to the volume irreversibly reduces the resolution and
would have to be very highres to have a hope of representing more than
two compartments.
cheers
Bruce
On Tue, 20 Nov 2018, ts...@rcmd.org wrote:
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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:
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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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