Hi experts,
I just want to know a way to extract the coordinates from a ROI mgh file.
I know that I can load the file with tksurfer but I have 100 .mgh files so if I could run a command line to have the coordinates in a .txt file or in a .m it would be helpful.
Thank you, Redwan
mri_cor2label with extract the coordinates into a label file. The coordinates will be in "tkregisterRAS". What coordinate system do you want? See
See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 07/25/2017 07:32 PM, Redwan Maatoug wrote:
Hi experts,
I just want to know a way to extract the coordinates from a ROI mgh file.
I know that I can load the file with tksurfer but I have 100 .mgh files so if I could run a command line to have the coordinates in a .txt file or in a .m it would be helpful.
Thank you, Redwan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thank you for your reply, I have used the tool *surf_cluster* to have the MNI coordinates. Is it a good alternative to *mri_cor2label *?
Thank you very much, Regards, Redwan
On Wed, Jul 26, 2017 at 2:41 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
mri_cor2label with extract the coordinates into a label file. The coordinates will be in "tkregisterRAS". What coordinate system do you want? See
See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 07/25/2017 07:32 PM, Redwan Maatoug wrote:
Hi experts,
I just want to know a way to extract the coordinates from a ROI mgh file.
I know that I can load the file with tksurfer but I have 100 .mgh files so if I could run a command line to have the coordinates in a .txt file or in a .m it would be helpful.
Thank you, Redwan
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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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.
Hi I would like to extract cooridantes of "aparc.a2009s+aseg.mgz" file. This file is stored in the mri folder. Would you please help me in this regards?
kind regards Mamun
On Thu, Jul 27, 2017 at 9:36 AM, Redwan Maatoug redwanmaatoug@gmail.com wrote:
Hi Doug,
Thank you for your reply, I have used the tool *surf_cluster* to have the MNI coordinates. Is it a good alternative to *mri_cor2label *?
Thank you very much, Regards, Redwan
On Wed, Jul 26, 2017 at 2:41 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
mri_cor2label with extract the coordinates into a label file. The coordinates will be in "tkregisterRAS". What coordinate system do you want? See
See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 07/25/2017 07:32 PM, Redwan Maatoug wrote:
Hi experts,
I just want to know a way to extract the coordinates from a ROI mgh
file.
I know that I can load the file with tksurfer but I have 100 .mgh files so if I could run a command line to have the coordinates in a .txt file or in a .m it would be helpful.
Thank you, Redwan
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
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.
Use mri_annotation2label to create a label, which will have tkregisterRAS coordinates
On 07/26/2017 08:32 PM, Md. Mamun Al-Amin wrote:
Hi I would like to extract cooridantes of "aparc.a2009s+aseg.mgz" file. This file is stored in the mri folder. Would you please help me in this regards?
kind regards Mamun
On Thu, Jul 27, 2017 at 9:36 AM, Redwan Maatoug <redwanmaatoug@gmail.com mailto:redwanmaatoug@gmail.com> wrote:
Hi Doug, Thank you for your reply, I have used the tool *surf_cluster* to have the MNI coordinates. Is it a good alternative to *mri_cor2label *? Thank you very much, Regards, Redwan On Wed, Jul 26, 2017 at 2:41 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: mri_cor2label with extract the coordinates into a label file. The coordinates will be in "tkregisterRAS". What coordinate system do you want? See See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems <https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems> On 07/25/2017 07:32 PM, Redwan Maatoug wrote: > Hi experts, > > I just want to know a way to extract the coordinates from a ROI mgh file. > > I know that I can load the file with tksurfer but I have 100 .mgh > files so if I could run a command line to have the coordinates in a > .txt file or in a .m it would be helpful. > > Thank you, > Redwan > > > _______________________________________________ > 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> -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <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 <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.--
Kind regards
Md. Mamun Al-Amin
PhD Candidate, Queensland Brain Institute Building 79, St Lucia QLD 4072
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yea, that works too
On 07/26/2017 07:36 PM, Redwan Maatoug wrote:
Hi Doug,
Thank you for your reply, I have used the tool *surf_cluster* to have the MNI coordinates. Is it a good alternative to *mri_cor2label *?
Thank you very much, Regards, Redwan
On Wed, Jul 26, 2017 at 2:41 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
mri_cor2label with extract the coordinates into a label file. The coordinates will be in "tkregisterRAS". What coordinate system do you want? See See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems <https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems> On 07/25/2017 07:32 PM, Redwan Maatoug wrote: > Hi experts, > > I just want to know a way to extract the coordinates from a ROI mgh file. > > I know that I can load the file with tksurfer but I have 100 .mgh > files so if I could run a command line to have the coordinates in a > .txt file or in a .m it would be helpful. > > Thank you, > Redwan > > > _______________________________________________ > 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> -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <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 <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
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Md. Mamun Al-Amin -
Redwan Maatoug