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Dear Community,
I am new to the software, so please bare with my ignorance! I have a triangular meshes of both hemispheres that were created not in FS but in another mesh generating software. I converted them with nibabel into two .pial files. When I run a 'read' command on them, I see the same structure as I see on native .pial file: [image: image.png]
Previously I have already run a recon-all on the MRI data I have and generated lh/rh.pial files. I also run -localGI on them, and also got the results just fine. Every time I work on the same computer. THe meshes that I converted with nibabel look the same (except for transcription) as the one I got from MRI. I cannot distinguish them in Freeview. But when I try to get lGI I got the error message. The command I use : recon-all -s name -localGI THe error I got:
I will attached the log file for more information. FS version I am using: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
I will be very grateful for any tips what this error is about, as I cannot find any reference about it anywhere.
Thank you for you time! Yana
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If you replaced the lh.pial and rh.pial files with different ones generated in another software, the vertex counts in these files will almost certainly not match the number of vertices (and faces) of all the other surfaces generated by FreeSurfer (?h.white etc) -- even if the surfaces look similar to the FreeSurfer ones on a macro scale.
You can read them in nibabel and try it.
I doubt that lgi computation is supposed to work if the vertex counts don't match.
Tim
On May 4, 2020 at 2:47 AM Yana Hoboken forad.hobo@gmail.com wrote:
External Email - Use CautionDear Community,
I am new to the software, so please bare with my ignorance! I have a triangular meshes of both hemispheres that were created not in FS but in another mesh generating software. I converted them with nibabel into two .pial files. When I run a 'read' command on them, I see the same structure as I see on native .pial file: [image: image.png]
Previously I have already run a recon-all on the MRI data I have and generated lh/rh.pial files. I also run -localGI on them, and also got the results just fine. Every time I work on the same computer. THe meshes that I converted with nibabel look the same (except for transcription) as the one I got from MRI. I cannot distinguish them in Freeview. But when I try to get lGI I got the error message. The command I use : recon-all -s name -localGI THe error I got:
I will attached the log file for more information. FS version I am using: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
I will be very grateful for any tips what this error is about, as I cannot find any reference about it anywhere.
Thank you for you time! Yana _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
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Hello!
Thank you for the tip!
As i understand it, -lGI has only one input which is pial surface. I am running it without any other files in the subject directory, I only have Subject- Name_-Surf- ?h.pial files when I attempt to execute the -lGI on it. So theoretically I do not have any other files to compare vertices count or any other parameter with my input file.
Thank you for your time! Will appreciate any help. Yana
On Mon, May 4, 2020 at 5:20 AM Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use CautionIf you replaced the lh.pial and rh.pial files with different ones generated in another software, the vertex counts in these files will almost certainly not match the number of vertices (and faces) of all the other surfaces generated by FreeSurfer (?h.white etc) -- even if the surfaces look similar to the FreeSurfer ones on a macro scale.
You can read them in nibabel and try it.
I doubt that lgi computation is supposed to work if the vertex counts don't match.
Tim
On May 4, 2020 at 2:47 AM Yana Hoboken forad.hobo@gmail.com wrote:
External Email - Use CautionDear Community,
I am new to the software, so please bare with my ignorance! I have a triangular meshes of both hemispheres that were created not in
FS
but in another mesh generating software. I converted them with nibabel
into
two .pial files. When I run a 'read' command on them, I see the same structure as I see on native .pial file: [image: image.png]
Previously I have already run a recon-all on the MRI data I have and generated lh/rh.pial files. I also run -localGI on them, and also got the results just fine. Every time I work on the same computer. THe meshes that I converted with nibabel look the same (except for transcription) as the one I got from MRI. I cannot distinguish them in Freeview. But when I try to get lGI I got the error message. The command I use : recon-all -s name -localGI THe error I got:
I will attached the log file for more information. FS version I am using: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
I will be very grateful for any tips what this error is about, as I
cannot
find any reference about it anywhere.
Thank you for you time! Yana _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Tim Schäfer -
Yana Hoboken