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
