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-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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
