you can just mri_convert lh.template_angle.mgz lh.template_angle_MW.nii
not, mri_convert, not mris_convert On 07/25/2017 04:16 PM, Yagmur Ozdemir 19 wrote: > mris_convert -c lh.template_angle.mgz lh.template_angle.mgz > lh.template_angle_MW.nii > > Thank you for 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 > > -- 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
