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
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
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 inesb@student.ethz.ch wrote:
External Email - Use CautionDear 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
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+ml@rcmd.org wrote:
External Email - Use CautionAs 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 inesb@student.ethz.ch wrote:
External Email - Use CautionDear 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
freesurfer@nmr.mgh.harvard.edu
-
Borges Pereira Ines Isabel -
Bruce Fischl -
ts+ml＠rcmd.org