Re: [Freesurfer] Quality of surface-based alignment
What criteria would you use to determine one alignment was better than another? Peace, Matt. From: Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, November 4, 2014 at 7:17 AM To: Freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Quality of surface-based alignment Hi Freesurfers, I was wondering whether there is a good way to assess post-hoc how well the alignment between two surfaces was. I wouldn't like to run the alignment again, but I could, if necessary. I would like to compare this alignment to a bunch of other alignments to see whether it was worse than the others. Thanks, Caspar ___ 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] Quality of surface-based alignment
Hi Caspar the easiest way it so look at the parcellations and see if they are accurate. Note that we do subject-to-atlas alignment, not subject-to-subject (you get the latter by composing two atlas transforms) cheers Bruce On Tue, 4 Nov 2014, Caspar M. Schwiedrzik wrote: Hi Freesurfers, I was wondering whether there is a good way to assess post-hoc how well the alignment between two surfaces was. I wouldn't like to run the alignment again, but I could, if necessary. I would like to compare this alignment to a bunch of other alignments to see whether it was worse than the others. Thanks, Caspar ___ 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] Quality of surface-based alignment
Hi Bruce and Matt, I should specify that I am working with non-human primate data, so unfortunately, looking at the parcellations would not work. I am aligning individuals to a a custom template that I made. I was wondering whether there is maybe an output file that has something numerical on how much one surface had to be transformed to be aligned to the other. I could alternatively compute the square difference between the two surfaces, or something like that. Thanks! Caspar 2014-11-04 11:19 GMT-05:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar the easiest way it so look at the parcellations and see if they are accurate. Note that we do subject-to-atlas alignment, not subject-to-subject (you get the latter by composing two atlas transforms) cheers Bruce On Tue, 4 Nov 2014, Caspar M. Schwiedrzik wrote: Hi Freesurfers, I was wondering whether there is a good way to assess post-hoc how well the alignment between two surfaces was. I wouldn't like to run the alignment again, but I could, if necessary. I would like to compare this alignment to a bunch of other alignments to see whether it was worse than the others. Thanks, Caspar ___ 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] Quality of surface-based alignment
You can look at how well the curvature and/or sulcal maps from your template overlay on the individual. doug On 11/04/2014 11:46 AM, Caspar M. Schwiedrzik wrote: Hi Bruce and Matt, I should specify that I am working with non-human primate data, so unfortunately, looking at the parcellations would not work. I am aligning individuals to a a custom template that I made. I was wondering whether there is maybe an output file that has something numerical on how much one surface had to be transformed to be aligned to the other. I could alternatively compute the square difference between the two surfaces, or something like that. Thanks! Caspar 2014-11-04 11:19 GMT-05:00 Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu: Hi Caspar the easiest way it so look at the parcellations and see if they are accurate. Note that we do subject-to-atlas alignment, not subject-to-subject (you get the latter by composing two atlas transforms) cheers Bruce On Tue, 4 Nov 2014, Caspar M. Schwiedrzik wrote: Hi Freesurfers, I was wondering whether there is a good way to assess post-hoc how well the alignment between two surfaces was. I wouldn't like to run the alignment again, but I could, if necessary. I would like to compare this alignment to a bunch of other alignments to see whether it was worse than the others. Thanks, Caspar ___ 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] Quality of surface-based alignment
oh, I see. I would paint the folding patterns on the sphere.reg and toggle back and forth between them to see if they look right. Alternatively you could draw some sulci onto one of your datasets (this is easy to do in tksurfer) and use mri_label2label to map it to others and see if they land in the right place (central sulcus, calcarine, sylvian, etc...) On Tue, 4 Nov 2014, Caspar M. Schwiedrzik wrote: Hi Bruce and Matt, I should specify that I am working with non-human primate data, so unfortunately, looking at the parcellations would not work. I am aligning individuals to a a custom template that I made. I was wondering whether there is maybe an output file that has something numerical on how much one surface had to be transformed to be aligned to the other. I could alternatively compute the square difference between the two surfaces, or something like that. Thanks! Caspar 2014-11-04 11:19 GMT-05:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar the easiest way it so look at the parcellations and see if they are accurate. Note that we do subject-to-atlas alignment, not subject-to-subject (you get the latter by composing two atlas transforms) cheers Bruce On Tue, 4 Nov 2014, Caspar M. Schwiedrzik wrote: Hi Freesurfers, I was wondering whether there is a good way to assess post-hoc how well the alignment between two surfaces was. I wouldn't like to run the alignment again, but I could, if necessary. I would like to compare this alignment to a bunch of other alignments to see whether it was worse than the others. Thanks, Caspar ___ 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
Re: [Freesurfer] Quality of surface-based alignment
Thanks! But there is nothing like a number I could pull from the registration process, e.g. the distances of the vertices in registration space? Caspar 2014-11-04 11:51 GMT-05:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: oh, I see. I would paint the folding patterns on the sphere.reg and toggle back and forth between them to see if they look right. Alternatively you could draw some sulci onto one of your datasets (this is easy to do in tksurfer) and use mri_label2label to map it to others and see if they land in the right place (central sulcus, calcarine, sylvian, etc...) On Tue, 4 Nov 2014, Caspar M. Schwiedrzik wrote: Hi Bruce and Matt, I should specify that I am working with non-human primate data, so unfortunately, looking at the parcellations would not work. I am aligning individuals to a a custom template that I made. I was wondering whether there is maybe an output file that has something numerical on how much one surface had to be transformed to be aligned to the other. I could alternatively compute the square difference between the two surfaces, or something like that. Thanks! Caspar 2014-11-04 11:19 GMT-05:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar the easiest way it so look at the parcellations and see if they are accurate. Note that we do subject-to-atlas alignment, not subject-to-subject (you get the latter by composing two atlas transforms) cheers Bruce On Tue, 4 Nov 2014, Caspar M. Schwiedrzik wrote: Hi Freesurfers, I was wondering whether there is a good way to assess post-hoc how well the alignment between two surfaces was. I wouldn't like to run the alignment again, but I could, if necessary. I would like to compare this alignment to a bunch of other alignments to see whether it was worse than the others. Thanks, Caspar ___ 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 ___ 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.
