Don't use --projopt and it won't segfault On 04/03/2014 02:08 AM, Joerg Pfannmoeller wrote: > The command is: > > mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject > subjid --interp nearest --projopt /.../map001 --hemi rh --o > /.../f001_surf.nii --noreshape --cortex > > The output is the follwoing: > > > srcvol = /.../f001.nii > srcreg = /.../register.f001.dof6.dat > srcregold = 0 > srcwarp unspecified > surf = white > hemi = rh > trgsubject = subjid > surfreg = sphere.reg > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > Loading label /.../label/rh.cortex.label > Reading surface /.../surf/rh.white > Done reading source surface > Reading thickness /.../surf/rh.thickness > Done > Mapping Source Volume onto Source Subject Surface > reading gm volume fraction from /.../map001.gm.mgz > reading wm volume fraction from /.../map001.wm.mgz > reading csf volume fraction from /.../map001.csf.mgz > mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject > subjid --interp nearest --projopt /.../map001 --hemi rh --o > /.../f001_surf.nii --noreshape --cortex: Segmentation fault > > Do you have an idea about the cause of the error? > > > > > > On Wed, 02 Apr 2014 17:28:14 -0400 > Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > >> what is your command line that is seg faulting? What is the terminal output? >> >> On 04/02/2014 05:17 PM, pfannmo...@uni-greifswald.de wrote: >>> Please help me with this issue: >>> >>> If I apply mri_surf2vol to a single volume of unprocessed epi-data, it >>> results in a segmentation fault. It works if I apply mri_vol2vol for >>> registration of epi and anatomy, but than an interpolation is >>> involved. I would like to avoid the interpolation and apply >>> mri_surf2vol directly to the unprocessed data in order to minimize the >>> number of interpolations. >>> >>> >>> At Wednesday, 02-04-2014 on 21:08 Douglas N Greve wrote: >>> >>> This is something BF added Sept 1 2009: >>> >>> added --projopt switch to do optimal linear estimation of gray matter >>> values given a set of precomputed gray matter densities. >>> >>> I don't know what it would mean beyond that >>> >>> doug >>> >>> >>> On 04/02/2014 10:49 AM, Joerg Pfannmoeller wrote: >>> > Hello, >>> > >>> > I found an option in mri_vol2surf for which I could not find a >>> documentation. The option is called: >>> > >>> > --projopt >>> > >>> > It would be nice if somebody could give a description of this >>> option. >>> > >>> > Respectfully yours >>> > >>> > pfannmoe >>> > >>> > >>> > _______________________________________________ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu >>> <mailto: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 <mailto: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 <mailto: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 >> -- >> 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 >
-- 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
