Allright, if the option --interp nearest is used the output is as given in a previous post (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35148.html). After applying --interp trilin the output is:
mri_vol2surf --mov /.../f001.nii --reg /.../register.f001.dof6.dat --interp trilin --projopt /.../map --hemi rh --o /.../f001_surf.nii --noreshape --cortex srcvol = /.../f001.nii srcreg = /.../register.f001.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh reshape = 0 interp = trilin 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 /.../map.gm.mgz reading wm volume fraction from /.../map.wm.mgz reading csf volume fraction from /.../map.csf.mgz mri_vol2surf --mov /.../f001.nii --reg /.../register.f001.dof6.dat --interp trilin --projopt /.../map --hemi rh --o /.../f001_surf.nii --noreshape --cortex: Segmentation fault If the option --interp is dissmissed completely the output is: mri_vol2surf --mov /.../f001.nii --reg /.../register.f001.dof6.dat --projopt /.../map --hemi rh --o /.../f001_surf.nii --noreshape --cortex srcvol = /.../f001.nii srcreg = /.../register.f001.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh 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 /.../map.gm.mgz reading wm volume fraction from /.../map.wm.mgz reading csf volume fraction from /.../map.csf.mgz mri_vol2surf --mov /.../f001.nii --reg /.../register.f001.dof6.dat --projopt /.../map --hemi rh --o /.../f001_surf.nii --noreshape --cortex: Segmentation fault Voxel size of the epi and the map data from mri_compute_volume_fractions is 1.5 x 1.5 x 2 mm^3 and of the t1 image is 1 x 1 x 1 mm^3. On Mon, 14 Apr 2014 12:24:37 -0400 Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > Can you send your commandline with --interp as well as the terminal output? > > On 04/14/2014 06:54 AM, Joerg Pfannmoeller wrote: > > Well, there is no difference between trilin or nearest. mri_vol2surf > > displays segfault regardless which option I use (trilin or nearest). > > > > > > On Thu, 10 Apr 2014 11:30:38 -0400 > > Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > > >> I don't understand what the question is. If you need to interpolate, > >> then use --interp trilinear > >> doug > >> > >> On 04/10/2014 04:36 AM, Joerg Pfannmoeller wrote: > >>> Allright! The only point I would like to emphasize is: > >>> > >>> Regardless if option trilin or nearest is used I need to interpolate the > >>> functional data to the structural image of the subject. This might be due > >>> to a feature of the function "build_sample_array" in the "mri_vol2surf" > >>> source code. In this function there are some constant values (din = 1.0, > >>> dout = 0.1, nsamples = 10), which might be the reason why I need to > >>> interpolate the functional data to the structural image. Currently I can > >>> not investigate the code any further. Do you have enough experience with > >>> the source code to clarify this question? > >>> > >>> On Wed, 09 Apr 2014 09:31:57 -0400 > >>> Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > >>> > >>>> You can use --projfrac (which can perform an interpolation with --interp > >>>> trilinear) > >>>> > >>>> > >>>> On 4/9/14 2:44 AM, Joerg Pfannmoeller wrote: > >>>>> Sorry for this question, but now I am confused. Do you mean that I > >>>>> should not use projopt and just use the interpolation? If so why should > >>>>> I not use projfrac? > >>>>> > >>>>> > >>>>> On Tue, 08 Apr 2014 15:02:36 -0400 > >>>>> Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > >>>>> > >>>>>> 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 > >>>> _______________________________________________ > >>>> 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
