You'll have to do without it for now and just do the interpolation On 04/08/2014 03:32 AM, Joerg Pfannmoeller wrote: > Well, I need to use that option. In this case I will just interpolate to the > 1 mm grid and proceed this way. > > > On Mon, 07 Apr 2014 12:14:47 -0400 > Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > >> Sorry, I don't understand. You mean it still segfaults without --projopt >> or that you have to use projopt? >> >> On 04/07/2014 02:36 AM, Joerg Pfannmoeller wrote: >>> Unfortunately that is no option for me. >>> >>> >>> >>> On Fri, 04 Apr 2014 15:33:47 -0400 >>> Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: >>> >>>> 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 >>> _______________________________________________ >>> 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
