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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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
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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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