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
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:
--projoptIt would be nice if somebody could give a description of this option.
Respectfully yours
pfannmoe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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
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
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
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
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.
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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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-- 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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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/
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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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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/
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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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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/
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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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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
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
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
However, let's forget about this question. I need to address something else and until that is finished it does not matter.
On Mon, 14 Apr 2014 12:54:30 +0200 Joerg Pfannmoeller pfannmoelj@uni-greifswald.de 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
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/
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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/
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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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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. 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/
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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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it sounds cool! I wonder what it does?
Actually, this uses mri_compute_volume_fractions and mri_compute_intensities to build partial-volume models of the tissue and then estimate them with projopt. I haven't tried this code in a few years so you are somewhat on your own. We are hoping to clean it up and release it when I find the time.
cheers Bruce
On Wed, 2 Apr 2014, 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:
--projoptIt would be nice if somebody could give a description of this option.
Respectfully yours
pfannmoe
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Bruce Fischl -
Douglas Greve -
Douglas N Greve
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Joerg Pfannmoeller -
pfannmoelj＠uni-greifswald.de