[Freesurfer] labels export
Hello FreeSurfers,Does any one of you know if exist a function to export labels as a ROI format?Regards,Gabriel-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ 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.
Re: [Freesurfer] labels export
Hi Gabriel, Have you tried mri_label2vol? If you want the volume in the anatomical space: mri_label2vol --label labelname.label --temp .nii.gz --identity --o volumename.nii.gz If you want it in some other space, you can specify the registration matrix using --reg and the template using --temp. Hope that helps, Priti > Hello > FreeSurfers,Does any one of you know if exist > a function to export labels as a ROI format? />Regards,Gabriel-- />--PhD. student > Gabriel González-EscamillaLaboratory of Functional Neuroscience />Department of Physiology, Anatomy, and Cell BiologyUniversity > Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- > Spain -Email: ggon...@upo.es />http://www.upo.es/neuroaging/es/ > ___ > 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 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.
Re: [Freesurfer] labels export
Thanks Priti,I've thought about that before, but actually I'm looking for literally .roi images, do you know if is this format possible from FS?Regards,GabrielEl 24/04/12, Priti Srinivasan escribió:Hi Gabriel,Have you tried mri_label2vol?If you want the volume in the anatomical space:mri_label2vol --label labelname.label --temp .nii.gz--identity --o volumename.nii.gzIf you want it in some other space, you can specify the registrationmatrix using --reg and the template using --temp.Hope that helps,Priti> Hello> FreeSurfers,Does any one of you know if exist> a function to export labels as a ROI format?> />Regards,Gabriel-- > />--PhD. student> Gabriel González-EscamillaLaboratory of Functional Neuroscience> />Department of Physiology, Anatomy, and Cell BiologyUniversity> Pablo de OlavideCtra. de Utrera, Km.141013 - Seville-> Spain -Email: ggon...@upo.es> />http://www.upo.es/neuroaging/es/> ___> Freesurfer mailing list> Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ 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.
Re: [Freesurfer] labels export
I don't think so. What is .roi format? On 04/24/2012 12:21 PM, Gabriel Gonzalez Escamilla wrote: > Thanks Priti, > > I've thought about that before, but actually I'm looking for literally > .roi images, do you know if is this format possible from FS? > > Regards, > Gabriel > > > > El 24/04/12, *Priti Srinivasan * escribió: >> Hi Gabriel, >> >> Have you tried mri_label2vol? >> >> If you want the volume in the anatomical space: >> >> mri_label2vol --label labelname.label --temp .nii.gz >> --identity --o volumename.nii.gz >> >> If you want it in some other space, you can specify the registration >> matrix using --reg and the template using --temp. >> >> Hope that helps, >> Priti >> >> >> >> > Hello >> > FreeSurfers,Does any one of you know if >> exist >> > a function to export labels as a ROI format?> > />Regards,Gabriel-- > > />--PhD. >> student >> > Gabriel González-EscamillaLaboratory of Functional >> Neuroscience> > />Department of Physiology, Anatomy, and Cell BiologyUniversity >> > Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- >> > Spain -Email: ggon...@upo.es> > />http://www.upo.es/neuroaging/es/ >> > ___ >> > 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 >> >> >> 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. >> > > -- > -- > PhD. student Gabriel González-Escamilla > Laboratory of Functional Neuroscience > Department of Physiology, Anatomy, and Cell Biology > University Pablo de Olavide > Ctra. de Utrera, Km.1 > 41013 - Seville > - Spain - > > Email: ggon...@upo.es > http://www.upo.es/neuroaging/es/ > > > ___ > 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 gr...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] labels export
they are just ascii files so it should be easy enough to do yourself On Tue, 24 Apr 2012, Gabriel Gonzalez Escamilla wrote: Thanks Priti, I've thought about that before, but actually I'm looking for literally .roi images, do you know if is this format possible from FS? Regards, Gabriel El 24/04/12, Priti Srinivasan escribió: Hi Gabriel, Have you tried mri_label2vol? If you want the volume in the anatomical space: mri_label2vol --label labelname.label --temp .nii.gz --identity --o volumename.nii.gz If you want it in some other space, you can specify the registration matrix using --reg and the template using --temp. Hope that helps, Priti > Hello > FreeSurfers,Does any one of you know if exist > a function to export labels as a ROI format? />Regards,Gabriel-- />--PhD. student > Gabriel González-EscamillaLaboratory of Functional Neuroscience />Department of Physiology, Anatomy, and Cell BiologyUniversity > Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- > Spain -Email: ggon...@upo.es />http://www.upo.es/neuroaging/es/ > ___ > 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 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. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ 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.
Re: [Freesurfer] labels export
And what about exporting as obj format, I have found a function to transform surfaces to obj, is it possible something like this but with the labels?Regards,GabrielEl 24/04/12, Bruce Fischl escribió:they are just ascii files so it should be easy enough to do yourselfOn Tue, 24 Apr 2012, Gabriel Gonzalez Escamilla wrote:>Thanks Priti,>>I've thought about that before, but actually I'm looking for literally .roi images, do you know if is this format possible from FS?>>Regards,>GabrielEl 24/04/12, Priti Srinivasan escribió:> Hi Gabriel,>> Have you tried mri_label2vol?>> If you want the volume in the anatomical space:>> mri_label2vol --label labelname.label --temp .nii.gz> --identity --o volumename.nii.gz>> If you want it in some other space, you can specify the registration> matrix using --reg and the template using --temp.>> Hope that helps,> Priti > Hello> > FreeSurfers,Does any one of you know if exist> > a function to export labels as a ROI format?> > />Regards,Gabriel-- > > />--PhD. student> > Gabriel González-EscamillaLaboratory of Functional Neuroscience> > />Department of Physiology, Anatomy, and Cell BiologyUniversity> > Pablo de OlavideCtra. de Utrera, Km.141013 - Seville-> > Spain -Email: ggon...@upo.es> > />http://www.upo.es/neuroaging/es/> > ___> > 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>>> 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.>>>-->-->PhD. student Gabriel González-Escamilla>Laboratory of Functional Neuroscience>Department of Physiology, Anatomy, and Cell Biology>University Pablo de Olavide>Ctra. de Utrera, Km.1>41013 - Seville>- Spain ->>Email: ggon...@upo.es>http://www.upo.es/neuroaging/es/>>-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ 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.
Re: [Freesurfer] labels export
Well I'mactually looking for something like convert the segmented structures, i.e. hippocampus, thalamus or putmen to an object or ROI file.Regards,GabrielEl 25/04/12, Gabriel Gonzalez Escamilla escribió:And what about exporting as obj format, I have found a function to transform surfaces to obj, is it possible something like this but with the labels?Regards,GabrielEl 24/04/12, Bruce Fischl escribió:they are just ascii files so it should be easy enough to do yourselfOn Tue, 24 Apr 2012, Gabriel Gonzalez Escamilla wrote:>Thanks Priti,>>I've thought about that before, but actually I'm looking for literally .roi images, do you know if is this format possible from FS?>>Regards,>GabrielEl 24/04/12, Priti Srinivasan escribió:> Hi Gabriel,>> Have you tried mri_label2vol?>> If you want the volume in the anatomical space:>> mri_label2vol --label labelname.label --temp .nii.gz> --identity --o volumename.nii.gz>> If you want it in some other space, you can specify the registration> matrix using --reg and the template using --temp.>> Hope that helps,> Priti > Hello> > FreeSurfers,Does any one of you know if exist> > a function to export labels as a ROI format?> > />Regards,Gabriel-- > > />--PhD. student> > Gabriel González-EscamillaLaboratory of Functional Neuroscience> > />Department of Physiology, Anatomy, and Cell BiologyUniversity> > Pablo de OlavideCtra. de Utrera, Km.141013 - Seville-> > Spain -Email: ggon...@upo.es> > />http://www.upo.es/neuroaging/es/> > ___> > 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>>> 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.>>>-->-->PhD. student Gabriel González-Escamilla>Laboratory of Functional Neuroscience>Department of Physiology, Anatomy, and Cell Biology>University Pablo de Olavide>Ctra. de Utrera, Km.1>41013 - Seville>- Spain ->>Email: ggon...@upo.es>http://www.upo.es/neuroaging/es/>>-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ -- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ 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.
Re: [Freesurfer] labels export
sorry, I don't know what obj format is either Bruce On Wed, 25 Apr 2012, Gabriel Gonzalez Escamilla wrote: And what about exporting as obj format, I have found a function to transform surfaces to obj, is it possible something like this but with the labels? Regards, Gabriel El 24/04/12, Bruce Fischl escribió: they are just ascii files so it should be easy enough to do yourself On Tue, 24 Apr 2012, Gabriel Gonzalez Escamilla wrote: >Thanks Priti, > >I've thought about that before, but actually I'm looking for literally .roi images, do you know if is this format possible from FS? > >Regards, >Gabriel > > > >El 24/04/12, Priti Srinivasan escribió: > Hi Gabriel, > > Have you tried mri_label2vol? > > If you want the volume in the anatomical space: > > mri_label2vol --label labelname.label --temp .nii.gz > --identity --o volumename.nii.gz > > If you want it in some other space, you can specify the registration > matrix using --reg and the template using --temp. > > Hope that helps, > Priti > > > > > Hello > > FreeSurfers,Does any one of you know if exist > > a function to export labels as a ROI format? > />Regards,Gabriel-- > />--PhD. student > > Gabriel González-EscamillaLaboratory of Functional Neuroscience > />Department of Physiology, Anatomy, and Cell BiologyUniversity > > Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- > > Spain -Email: ggon...@upo.es > />http://www.upo.es/neuroaging/es/ > > ___ > > 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 > > > 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. > > >-- >-- >PhD. student Gabriel González-Escamilla >Laboratory of Functional Neuroscience >Department of Physiology, Anatomy, and Cell Biology >University Pablo de Olavide >Ctra. de Utrera, Km.1 >41013 - Seville >- Spain - > >Email: ggon...@upo.es >http://www.upo.es/neuroaging/es/ > > -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ 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.
