[Freesurfer] Pial surface with point-to-point correspondance between subjects
Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ 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] Pial surface with point-to-point correspondance between subjects
Hi Alexandre can you tell us what you want to do with the point-to-point correspondence? We don't usually map surfaces into a common space since we want to have uniform resolution/sampling in the individual coords. cheers Bruce On Wed, 29 Oct 2014, Alexandre Routier wrote: Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ 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] Pial surface with point-to-point correspondance between subjects
Hello Bruce, I would like to build an atlas of subcortical structures and pial surface on my population of study. But given the anatomical complexity of the pial surface (and the number of points), I would like to use point-to-point correspondence so as to have a L^2 metric (I use another metric for subcortical structures). I don't know if I am clear enough but since I estimate the template and the variability between the template and the subjects, I would like to detect information such as atrophy thanks to the deformation parameters. Is there any solution? Alexandre 2014-10-29 13:49 GMT+01:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Alexandre can you tell us what you want to do with the point-to-point correspondence? We don't usually map surfaces into a common space since we want to have uniform resolution/sampling in the individual coords. cheers Bruce On Wed, 29 Oct 2014, Alexandre Routier wrote: Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ 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.
Re: [Freesurfer] Pial surface with point-to-point correspondance between subjects
I'm not sure what you mean by working with the pial surfaces with respect to point-to-point correspondence. Can you give more info? doug On 10/29/2014 06:29 AM, Alexandre Routier wrote: Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ 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: 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.
Re: [Freesurfer] Pial surface with point-to-point correspondance between subjects
What I wanted to say is that there is the exact number of points of the pial surface for each subject and if I look to the i-th vertex of the pial surface of a given subject, it should be located on the same area for another subject. Alexandre 2014-10-29 15:25 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: I'm not sure what you mean by working with the pial surfaces with respect to point-to-point correspondence. Can you give more info? doug On 10/29/2014 06:29 AM, Alexandre Routier wrote: Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ 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: 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.
Re: [Freesurfer] Pial surface with point-to-point correspondance between subjects
This is not something we support. On 10/29/2014 10:32 AM, Alexandre Routier wrote: What I wanted to say is that there is the exact number of points of the pial surface for each subject and if I look to the i-th vertex of the pial surface of a given subject, it should be located on the same area for another subject. Alexandre 2014-10-29 15:25 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: I'm not sure what you mean by working with the pial surfaces with respect to point-to-point correspondence. Can you give more info? doug On 10/29/2014 06:29 AM, Alexandre Routier wrote: Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ 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 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 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 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/ ___ 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 gr...@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
Re: [Freesurfer] Pial surface with point-to-point correspondance between subjects
Oh, okay. I thought this kind of data could be obtained since it exists for longitudinal analysis. Thanks for your answer anyway! 2014-10-29 15:35 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: This is not something we support. On 10/29/2014 10:32 AM, Alexandre Routier wrote: What I wanted to say is that there is the exact number of points of the pial surface for each subject and if I look to the i-th vertex of the pial surface of a given subject, it should be located on the same area for another subject. Alexandre 2014-10-29 15:25 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: I'm not sure what you mean by working with the pial surfaces with respect to point-to-point correspondence. Can you give more info? doug On 10/29/2014 06:29 AM, Alexandre Routier wrote: Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ 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 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 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 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/ ___ 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 gr...@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 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] Pial surface with point-to-point correspondance between subjects
you can just compute the jacobian of the ?h.sphere.reg for deformation. I'm not sure I understand how you would use an L2 metric. There are tools in AFNI/SUMA for converting a freesurfer surface to a standard mesh that you could use cheers Bruce On Wed, 29 Oct 2014, Alexandre Routier wrote: Hello Bruce, I would like to build an atlas of subcortical structures and pial surface on my population of study. But given the anatomical complexity of the pial surface (and the number of points), I would like to use point-to-point correspondence so as to have a L^2 metric (I use another metric for subcortical structures). I don't know if I am clear enough but since I estimate the template and the variability between the template and the subjects, I would like to detect information such as atrophy thanks to the deformation parameters. Is there any solution? Alexandre 2014-10-29 13:49 GMT+01:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Alexandre can you tell us what you want to do with the point-to-point correspondence? We don't usually map surfaces into a common space since we want to have uniform resolution/sampling in the individual coords. cheers Bruce On Wed, 29 Oct 2014, Alexandre Routier wrote: Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ 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.
Re: [Freesurfer] Pial surface with point-to-point correspondance between subjects
no, but I think SUMA does. Check it out. I'll cc Ziad so he can chime in. cheers Bruce On Wed, 29 Oct 2014, Douglas N Greve wrote: This is not something we support. On 10/29/2014 10:32 AM, Alexandre Routier wrote: What I wanted to say is that there is the exact number of points of the pial surface for each subject and if I look to the i-th vertex of the pial surface of a given subject, it should be located on the same area for another subject. Alexandre 2014-10-29 15:25 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: I'm not sure what you mean by working with the pial surfaces with respect to point-to-point correspondence. Can you give more info? doug On 10/29/2014 06:29 AM, Alexandre Routier wrote: Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ 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 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 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 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/ ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Pial surface with point-to-point correspondance between subjects
Okay, thanks for the answer, I'll have a look on this software. Alexandre 2014-10-29 16:05 GMT+01:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: no, but I think SUMA does. Check it out. I'll cc Ziad so he can chime in. cheers Bruce On Wed, 29 Oct 2014, Douglas N Greve wrote: This is not something we support. On 10/29/2014 10:32 AM, Alexandre Routier wrote: What I wanted to say is that there is the exact number of points of the pial surface for each subject and if I look to the i-th vertex of the pial surface of a given subject, it should be located on the same area for another subject. Alexandre 2014-10-29 15:25 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: I'm not sure what you mean by working with the pial surfaces with respect to point-to-point correspondence. Can you give more info? doug On 10/29/2014 06:29 AM, Alexandre Routier wrote: Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre ___ 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 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 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 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/ ___ 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 ___ 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.
