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