I just realized I needed lh.inflated in the command. I think it works now. Thank you for all the help!
Idil ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 11:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation Violation problem in surface files what is your command line? On 07/25/2017 03:52 PM, Yagmur Ozdemir 19 wrote: > 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 > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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
