[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

Re: [Freesurfer] Quality of surface-based alignment

@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

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

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

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

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

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