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 greve@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 greve@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 greve@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 greve@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 greve@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 greve@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 greve@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, pfannmoelj@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. 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Greve, Ph.D. >>>>>>>> MGH-NMR Center >>>>>>>> greve@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 >>>>>> greve@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 >>>> greve@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. 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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/
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