When I do either of the conversions with mris_convert, the system gives freadFloat: fread failed / No such file or directory then a Segmentation fault error.
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: Tuesday, July 25, 2017 10:21 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files 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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@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-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 > > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
