Don't use --projopt
On 04/15/2014 02:21 AM, Joerg Pfannmoeller wrote: > 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 > > -- 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
