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 <fischl@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
>       >
>       >
>       >
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