you can convert the overlays directly to nifti, but they aren't surfaces - they are scalar fields over the surface (that is, they are one value/location with no neighborhood info). Not sure what Brainvoyager supports, but you could convert the surfaces to gifti
cheers Bruce
On Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote:
I am trying to export the overlays in .mgz format to Brainvoyager which recognizes nifti or its native .vmr format. However the mri_convert command gives error when I try to convert the templates. I thought if I could save the overlays directly onto the inflated surface files I could convert then visualize them in Brainvoyager, but couldn't figure that out so far. Thank you for the help!
Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 7:47 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil
I'm not sure what you mean. If you give us a better idea of your overall goal we can give you more helpful answers I expect Bruce On Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote:
Bruce,
Thank you so much for the help! I guess then the way to export these overlays to other softwares is writing them on the subject's inflated surface file.
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, July 24, 2017 10:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil,
we only store surface overlays in .mgz not surfaces themselves. Try loading a surface (like lh.inflated) then load whatever you were looking at as an overlay on the surface cheers Bruce On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello freesurfer experts,
I am trying to use an occipital lobe template adapted to my data as several surface and volume files, and there seems to be a problem with the surface files. Whenever I try to open a surface overlay (in .mgz format) in freeview this error comes up;
freadFloat: fread failed freadFloat: fread failed ... [0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range ...
When I try to convert this file to nifti format a seemingly similar error comes up;
(...) mri_convert rh.template_areas.mgz AU_areas_template_rh.nii.gz mri_convert.bin rh.template_areas.mgz AU_areas_template_rh.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from rh.template_areas.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to AU_areas_template_rh.nii.gz... NIFTI FORMAT ERROR: nslices 117239 in volume exceeds 32768
I have tried to debug but failed so far. Has anyone come across a similar problem and do you have an opinion onto what might be causing this? The same adapted template's volume files work just fine.
--I am using Ubuntu 16.04& freesurfer v.6
Thank you so much! Idil
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