Dear list,
I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything.
mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype = trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_smoother_surf.mgz trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices
Cannot allocate memory Return code: 254
Any suggestions?
Thanks, john
Hi John,
It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are using the right command?
D
On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths j.davidgriffiths@gmail.com wrote:
Dear list,
I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything.
mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype = trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_smoother_surf.mgz trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices
Cannot allocate memory Return code: 254
Any suggestions?
Thanks, john
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surf2surf actually takes surface overlays (not surfaces themselves) as input, and they can be in any format that FS reads. The wiki is probably not up-to-date as those options are ok. doug
Daniel Wakeman wrote:
Hi John,
It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are using the right command?
D
On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths j.davidgriffiths@gmail.com wrote:
Dear list,
I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything.
mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype = trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_smoother_surf.mgz trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices
Cannot allocate memory Return code: 254
Any suggestions?
Thanks, john
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[ Douglas and Dan - sending this again as I didn't sent it to the list address before. Sorry. ]
Thanks guys.
When I run mri_info on the .mgz file I was using before it seems crash (nothing happens, and have to press ctrl+c to get the console back). So I suppose that partially explains mri_surf2surf not working. Not sure what's going wrong there - the command I used was
mris_convert /work/imaging5/Freesurfer/CBU070282/surf/lh.pial /home/jdg45/lh.pial_converted.mgz
For the original question - I was using a converted .mgz file because when I just give it the path to the 'lh.pial' file in the same directory it says it cant determine the file type -
mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /work/imaging5/Freesurfer/CBU070282/surf/lh.pial --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: ERROR: could not determine type of /work/imaging5/Freesurfer/CBU070282/surf/lh.pial Standard error:
Is there a .xxx suffix for those files I should be using? Incidentally, the reason I'm doing this is that I want to downsample a surface file; someone suggested to me to use mri_surf2surf with the 'trgicoorder' flag. Is this a good way to downsample a surface? Thanks, john
On 6 December 2011 19:02, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
surf2surf actually takes surface overlays (not surfaces themselves) as input, and they can be in any format that FS reads. The wiki is probably not up-to-date as those options are ok. doug
Daniel Wakeman wrote:
Hi John,
It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are using the right command?
D
On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths j.davidgriffiths@gmail.com wrote:
Dear list,
I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything.
mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /home/jdg45/lh.pial_converted.**mgz --tval /home/jdg45/CBU070282_**smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.**mgz srctype = trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_**smoother_surf.mgz trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/**CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices
Cannot allocate memory Return code: 254
Any suggestions?
Thanks, john
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Hi John
Doug can say for sure, but I think you want to give it the switch --sval-xyz so it knows to expect a surface not a scalar field over the surface.
cheers Bruce On Wed, 7 Dec 2011, John Griffiths wrote:
[ Douglas and Dan - sending this again as I didn't sent it to the list address before. Sorry. ]
Thanks guys. When I run mri_info on the .mgz file I was using before it seems crash (nothing happens, and have to press ctrl+c to get the console back). So I suppose that partially explains mri_surf2surf not working. Not sure what's going wrong there - the command I used was mris_convert /work/imaging5/Freesurfer/CBU070282/surf/lh.pial /home/jdg45/lh.pial_converted.mgz
For the original question - I was using a converted .mgz file because when I just give it the path to the 'lh.pial' file in the same directory it says it cant determine the file type - mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /work/imaging5/Freesurfer/CBU070282/surf/lh.pial --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: ERROR: could not determine type of /work/imaging5/Freesurfer/CBU070282/surf/lh.pial Standard error:
Is there a .xxx suffix for those files I should be using? Incidentally, the reason I'm doing this is that I want to downsample a surface file; someone suggested to me to use mri_surf2surf with the 'trgicoorder' flag. Is this a good way to downsample a surface? Thanks, john
On 6 December 2011 19:02, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
surf2surf actually takes surface overlays (not surfaces themselves) as input, and they can be in any format that FS reads. The wiki is probably not up-to-date as those options are ok. doug Daniel Wakeman wrote: Hi John, It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are using the right command? D On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths <j.davidgriffiths@gmail.com> wrote: Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype = trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_smoother_surf.mgz trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices Cannot allocate memory Return code: 254 Any suggestions? Thanks, john _______________________________________________ Freesurfer mailing list 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Yes, give it both --sval-xyz and --tval-xyz to indicate that the output is a surface. We usually use mris_smooth to smooth surfaces; I'm not sure whether this use of mri_surf2surf will work properly. doug
Bruce Fischl wrote:
Hi John
Doug can say for sure, but I think you want to give it the switch --sval-xyz so it knows to expect a surface not a scalar field over the surface.
cheers Bruce On Wed, 7 Dec 2011, John Griffiths wrote:
[ Douglas and Dan - sending this again as I didn't sent it to the list address before. Sorry. ]
Thanks guys.
When I run mri_info on the .mgz file I was using before it seems crash (nothing happens, and have to press ctrl+c to get the console back). So I suppose that partially explains mri_surf2surf not working. Not sure what's going wrong there - the command I used was mris_convert /work/imaging5/Freesurfer/CBU070282/surf/lh.pial /home/jdg45/lh.pial_converted.mgz
For the original question - I was using a converted .mgz file because when I just give it the path to the 'lh.pial' file in the same directory it says it cant determine the file type - mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /work/imaging5/Freesurfer/CBU070282/surf/lh.pial --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: ERROR: could not determine type of /work/imaging5/Freesurfer/CBU070282/surf/lh.pial Standard error:
Is there a .xxx suffix for those files I should be using? Incidentally, the reason I'm doing this is that I want to downsample a surface file; someone suggested to me to use mri_surf2surf with the 'trgicoorder' flag. Is this a good way to downsample a surface? Thanks, john
On 6 December 2011 19:02, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
surf2surf actually takes surface overlays (not surfaces themselves) as input, and they can be in any format that FS reads. The wiki is probably not up-to-date as those options are ok. doug Daniel Wakeman wrote: Hi John, It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are using the right command? D On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths <j.davidgriffiths@gmail.com> wrote: Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype = trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_smoother_surf.mgz trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices Cannot allocate memory Return code: 254 Any suggestions? Thanks, john _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Ok. Can't see any options in mris_smooth info reducing the number of vertices. How would I do that?
Ta, john
On 9 December 2011 17:22, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Yes, give it both --sval-xyz and --tval-xyz to indicate that the output is a surface. We usually use mris_smooth to smooth surfaces; I'm not sure whether this use of mri_surf2surf will work properly. doug
Bruce Fischl wrote:
Hi John
Doug can say for sure, but I think you want to give it the switch --sval-xyz so it knows to expect a surface not a scalar field over the surface.
cheers Bruce On Wed, 7 Dec 2011, John Griffiths wrote:
[ Douglas and Dan - sending this again as I didn't sent it to the list
address before. Sorry. ]
Thanks guys. When I run mri_info on the .mgz file I was using before it seems crash (nothing happens, and have to press ctrl+c to get the console back). So I suppose that partially explains mri_surf2surf not working. Not sure what's going wrong there - the command I used was mris_convert /work/imaging5/Freesurfer/**CBU070282/surf/lh.pial /home/jdg45/lh.pial_converted.**mgz
For the original question - I was using a converted .mgz file because when I just give it the path to the 'lh.pial' file in the same directory it says it cant determine the file type - mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /work/imaging5/Freesurfer/**CBU070282/surf/lh.pial --tval /home/jdg45/CBU070282_**smoother_surf.mgz --s CBU070282 Standard output: ERROR: could not determine type of /work/imaging5/Freesurfer/**CBU070282/surf/lh.pial Standard error:
Is there a .xxx suffix for those files I should be using? Incidentally, the reason I'm doing this is that I want to downsample a surface file; someone suggested to me to use mri_surf2surf with the 'trgicoorder' flag. Is this a good way to downsample a surface? Thanks, john
On 6 December 2011 19:02, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
surf2surf actually takes surface overlays (not surfaces themselves) as input, and they can be in any format that FS reads. The wiki is probably not up-to-date as those options are ok. doug Daniel Wakeman wrote: Hi John, It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are using the right command? D On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths <j.davidgriffiths@gmail.com> wrote: Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /home/jdg45/lh.pial_converted.**mgz --tval /home/jdg45/CBU070282_**smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.**mgz srctype = trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_**smoother_surf.mgz trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/**CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices
Cannot allocate memory Return code: 254 Any suggestions? Thanks, john ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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<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/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Bruce, do you have a command to reduce the number of vertices?
John Griffiths wrote:
Ok. Can't see any options in mris_smooth info reducing the number of vertices. How would I do that?
Ta, john
On 9 December 2011 17:22, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Yes, give it both --sval-xyz and --tval-xyz to indicate that the output is a surface. We usually use mris_smooth to smooth surfaces; I'm not sure whether this use of mri_surf2surf will work properly. doug Bruce Fischl wrote: Hi John Doug can say for sure, but I think you want to give it the switch --sval-xyz so it knows to expect a surface not a scalar field over the surface. cheers Bruce On Wed, 7 Dec 2011, John Griffiths wrote: [ Douglas and Dan - sending this again as I didn't sent it to the list address before. Sorry. ] Thanks guys. When I run mri_info on the .mgz file I was using before it seems crash (nothing happens, and have to press ctrl+c to get the console back). So I suppose that partially explains mri_surf2surf not working. Not sure what's going wrong there - the command I used was mris_convert /work/imaging5/Freesurfer/CBU070282/surf/lh.pial /home/jdg45/lh.pial_converted.mgz For the original question - I was using a converted .mgz file because when I just give it the path to the 'lh.pial' file in the same directory it says it cant determine the file type - mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /work/imaging5/Freesurfer/CBU070282/surf/lh.pial --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: ERROR: could not determine type of /work/imaging5/Freesurfer/CBU070282/surf/lh.pial Standard error: Is there a .xxx suffix for those files I should be using? Incidentally, the reason I'm doing this is that I want to downsample a surface file; someone suggested to me to use mri_surf2surf with the 'trgicoorder' flag. Is this a good way to downsample a surface? Thanks, john On 6 December 2011 19:02, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: surf2surf actually takes surface overlays (not surfaces themselves) as input, and they can be in any format that FS reads. The wiki is probably not up-to-date as those options are ok. doug Daniel Wakeman wrote: Hi John, It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are using the right command? D On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths <j.davidgriffiths@gmail.com <mailto:j.davidgriffiths@gmail.com>> wrote: Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype = trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_smoother_surf.mgz trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 <tel:2032167524> slices Cannot allocate memory Return code: 254 Any suggestions? Thanks, john _______________________________________________ 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 <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 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
not and keep the topology (there is some decimation that is used in the EEG/MEG inverse stuff, but it's just to generate points, not faces) On Fri, 9 Dec 2011, Douglas N Greve wrote:
Bruce, do you have a command to reduce the number of vertices?
John Griffiths wrote:
Ok. Can't see any options in mris_smooth info reducing the number of vertices. How would I do that?
Ta, john
On 9 December 2011 17:22, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Yes, give it both --sval-xyz and --tval-xyz to indicate that the output is a surface. We usually use mris_smooth to smooth surfaces; I'm not sure whether this use of mri_surf2surf will work properly. doug Bruce Fischl wrote: Hi John Doug can say for sure, but I think you want to give it the switch --sval-xyz so it knows to expect a surface not a scalar field over the surface. cheers Bruce On Wed, 7 Dec 2011, John Griffiths wrote: [ Douglas and Dan - sending this again as I didn't sent it to the list address before. Sorry. ] Thanks guys. When I run mri_info on the .mgz file I was using before it seems crash (nothing happens, and have to press ctrl+c to get the console back). So I suppose that partially explains mri_surf2surf not working. Not sure what's going wrong there - the command I used was mris_convert /work/imaging5/Freesurfer/CBU070282/surf/lh.pial /home/jdg45/lh.pial_converted.mgz For the original question - I was using a converted .mgz file because when I just give it the path to the 'lh.pial' file in the same directory it says it cant determine the file type - mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /work/imaging5/Freesurfer/CBU070282/surf/lh.pial --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: ERROR: could not determine type of /work/imaging5/Freesurfer/CBU070282/surf/lh.pial Standard error: Is there a .xxx suffix for those files I should be using? Incidentally, the reason I'm doing this is that I want to downsample a surface file; someone suggested to me to use mri_surf2surf with the 'trgicoorder' flag. Is this a good way to downsample a surface? Thanks, john On 6 December 2011 19:02, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: surf2surf actually takes surface overlays (not surfaces themselves) as input, and they can be in any format that FS reads. The wiki is probably not up-to-date as those options are ok. doug Daniel Wakeman wrote: Hi John, It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are using the right command? D On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths <j.davidgriffiths@gmail.com <mailto:j.davidgriffiths@gmail.com>> wrote: Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype = trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_smoother_surf.mgz trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 <tel:2032167524> slices Cannot allocate memory Return code: 254 Any suggestions? Thanks, john _______________________________________________ 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 <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 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
it won't On Fri, 9 Dec 2011, John Griffiths wrote:
Ok. Can't see any options in mris_smooth info reducing the number of vertices. How would I do that?
Ta, john
On 9 December 2011 17:22, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: Yes, give it both --sval-xyz and --tval-xyz to indicate that the output is a surface. We usually use mris_smooth to smooth surfaces; I'm not sure whether this use of mri_surf2surf will work properly. doug
Bruce Fischl wrote: Hi John Doug can say for sure, but I think you want to give it the switch --sval-xyz so it knows to expect a surface not a scalar field over the surface. cheers Bruce On Wed, 7 Dec 2011, John Griffiths wrote: [ Douglas and Dan - sending this again as I didn't sent it to the list address before. Sorry. ] Thanks guys. When I run mri_info on the .mgz file I was using before it seems crash (nothing happens, and have to press ctrl+c to get the console back). So I suppose that partially explains mri_surf2surf not working. Not sure what's going wrong there - the command I used was mris_convert /work/imaging5/Freesurfer/CBU070282/surf/lh.pial /home/jdg45/lh.pial_converted.mgz For the original question - I was using a converted .mgz file because when I just give it the path to the 'lh.pial' file in the same directory it says it cant determine the file type - mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /work/imaging5/Freesurfer/CBU070282/surf/lh.pial --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: ERROR: could not determine type of /work/imaging5/Freesurfer/CBU070282/surf/lh.pial Standard error: Is there a .xxx suffix for those files I should be using? Incidentally, the reason I'm doing this is that I want to downsample a surface file; someone suggested to me to use mri_surf2surf with the 'trgicoorder' flag. Is this a good way to downsample a surface? Thanks, john On 6 December 2011 19:02, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: surf2surf actually takes surface overlays (not surfaces themselves) as input, and they can be in any format that FS reads. The wiki is probably not up-to-date as those options are ok. doug Daniel Wakeman wrote: Hi John, It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are using the right command? D On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths <j.davidgriffiths@gmail.com> wrote: Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype = trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_smoother_surf.mgz trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices Cannot allocate memory Return code: 254 Any suggestions? Thanks, john _______________________________________________ Freesurfer mailing list 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
What is lh.pial_converted.mgz? How big is it? what do get if you run mri_info on it? doug
John Griffiths wrote:
Dear list,
I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything.
mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype = trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_smoother_surf.mgz trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices
Cannot allocate memory Return code: 254
Any suggestions?
Thanks, john
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