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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
