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. Greve, Ph.D. >>>>>>>> MGH-NMR Center >>>>>>>> greve@nmr.mgh.harvard.edu mailto: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 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 >>>>>>> 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. 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
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