yes, it's what i wanted to say.
On Aug 2, 2017 17:46, "Douglas Greve" greve@nmr.mgh.harvard.edu wrote:
what do you mean by referential? the coordinate system of the vertex coords?
On 8/2/17 4:49 AM, pierre deman-kibleur wrote:
Hi,
Is it possible to have the gifti output in the same referential as the orig nii file as well ? I tried mris_convert lh.white lh.white.gii -rl mri/orig/001.mgz but mris_convert doesn't have the -rl option.
Regards, Pierre
On Wed, Aug 10, 2016 at 2:40 PM, Iglesias, Eugenio e.iglesias@ucl.ac.uk wrote:
You can always run mri_convert with the -rl (“reslice like”) flag to achieve this. Something like: mri_convert input.mgz output.mgz -rl reference.mgz -odt float If it’s a segmentation volume, you should add -rt nearest, in order to use nearest neighbor interpolation. Cheers, Eugenio
Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
On 10 Aug 2016, at 13:31, pierre deman deman.pierre@gmail.com wrote:
Hello,
I am trying to have the atlases aparc.a2009+aseg.mgz, hippocampal subfield etc ... in a matrix with the same size as the input of recon-all (and not the cubic matrix 256x256x256) and with the same orientation.
what is the best way to do it ?
Cheers, Pierre
-- DEMAN Pierre Mobile : +33 7 82 57 80 94 <+33%207%2082%2057%2080%2094> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Try adding --to-scanner to the mris_convert command. I think you'll need v6
On 8/2/17 12:02 PM, pierre deman-kibleur wrote:
yes, it's what i wanted to say.
On Aug 2, 2017 17:46, "Douglas Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
what do you mean by referential? the coordinate system of the vertex coords? On 8/2/17 4:49 AM, pierre deman-kibleur wrote:Hi, Is it possible to have the gifti output in the same referential as the orig nii file as well ? I tried mris_convert lh.white lh.white.gii -rl mri/orig/001.mgz but mris_convert doesn't have the -rl option. Regards, Pierre On Wed, Aug 10, 2016 at 2:40 PM, Iglesias, Eugenio <e.iglesias@ucl.ac.uk <mailto:e.iglesias@ucl.ac.uk>> wrote: You can always run mri_convert with the -rl (“reslice like”) flag to achieve this. Something like: mri_convert input.mgz output.mgz -rl reference.mgz -odt float If it’s a segmentation volume, you should add -rt nearest, in order to use nearest neighbor interpolation. Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/On 10 Aug 2016, at 13:31, pierre deman <deman.pierre@gmail.com <mailto:deman.pierre@gmail.com>> wrote: Hello, I am trying to have the atlases aparc.a2009+aseg.mgz, hippocampal subfield etc ... in a matrix with the same size as the input of recon-all (and not the cubic matrix 256x256x256) and with the same orientation. what is the best way to do it ? Cheers, Pierre -- DEMAN Pierre Mobile : +33 7 82 57 80 94 <tel:+33%207%2082%2057%2080%2094> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <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 <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. -- DEMAN Pierre Mobile : +33 7 82 57 80 94 <tel:+33%207%2082%2057%2080%2094> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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
it seems to works thanks.
On Wed, Aug 2, 2017 at 6:20 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Try adding --to-scanner to the mris_convert command. I think you'll need v6
On 8/2/17 12:02 PM, pierre deman-kibleur wrote:
yes, it's what i wanted to say.
On Aug 2, 2017 17:46, "Douglas Greve" greve@nmr.mgh.harvard.edu wrote:
what do you mean by referential? the coordinate system of the vertex coords?
On 8/2/17 4:49 AM, pierre deman-kibleur wrote:
Hi,
Is it possible to have the gifti output in the same referential as the orig nii file as well ? I tried mris_convert lh.white lh.white.gii -rl mri/orig/001.mgz but mris_convert doesn't have the -rl option.
Regards, Pierre
On Wed, Aug 10, 2016 at 2:40 PM, Iglesias, Eugenio e.iglesias@ucl.ac.uk wrote:
You can always run mri_convert with the -rl (“reslice like”) flag to achieve this. Something like: mri_convert input.mgz output.mgz -rl reference.mgz -odt float If it’s a segmentation volume, you should add -rt nearest, in order to use nearest neighbor interpolation. Cheers, Eugenio
Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
On 10 Aug 2016, at 13:31, pierre deman deman.pierre@gmail.com wrote:
Hello,
I am trying to have the atlases aparc.a2009+aseg.mgz, hippocampal subfield etc ... in a matrix with the same size as the input of recon-all (and not the cubic matrix 256x256x256) and with the same orientation.
what is the best way to do it ?
Cheers, Pierre
-- DEMAN Pierre Mobile : +33 7 82 57 80 94 <+33%207%2082%2057%2080%2094> _______________________________________________ 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
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.
-- DEMAN Pierre Mobile : +33 7 82 57 80 94 <+33%207%2082%2057%2080%2094>
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e du/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/compli anceline . 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 listFreesurfer@nmr.mgh.harvard.eduhttps://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
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@nmr.mgh.harvard.edu
-
Douglas Greve -
pierre deman-kibleur