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
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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/
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/
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