Hi Doug,
I've run the steps outlined in the SurfaceRegAndTemplates page so far. So:
make_average_subject --out newtemplate --subjects subj1 subj2 subj3 ...
foreach subject (subj1 subj2 subj3 ...)
cd $SUBJECTS_DIR/subject
mris_register -curv surf/lh.sphere \
$SUBJECTS_DIR/newtemplate/lh.reg.template.tif \
surf/lh.sphere.reg.newtemplate
end
mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s subj3 ...
make_average_subject --out newnewtemplate --surf-reg
sphere.reg.newtemplate \
--subjects subj1 subj2 subj3 ...
My understanding is that the next step is to now register each individual
surface to this new template and then run through the surface (and volume)
labeling steps. Is that correct?
It occurs to me that the fsaverage template used as the target for any .gcs
that I would to label the surface. Will I have to account for this?
Thanks again,
Jason
On Thu, Mar 5, 2015 at 3:26 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
>
> If you used make_average_subject to create the template, you can run
> surfreg to do the registration. If/when you run mris_preproc, make sure
> to spec both the target subject and the new spherical registration
>
>
> On 03/05/2015 03:18 PM, Bruce Fischl wrote:
> > Hi Jason
> >
> > I don't think so - you'll probably have to edit the recon-all script. And
> > by template do you just mean the folding pattern .tif files, or do you
> > meant the parcellation atlases (*.gcs)?
> >
> > cheers
> > Bruce
> > On Thu, 5 Mar 2015, Jason Tourville
> > wrote:
> >
> >> Greetings,
> >> I have generated custom surface templates from pediatric data sets. To
> apply
> >> it to the larger data set, is it sufficient to simply run the autorecon3
> >> steps (perhaps skipping the mris_sphere step)? If so, is there a handy
> flag
> >> for running this with recon-all and/or a way to run autorecon3 with a
> flag
> >> indicating that the non-default template should be used?
> >>
> >> Once I've done this, I'd like to do some form of comparison b/w the
> >> templates. I am considering looking at the overlap of surface labels
> >> generated by the custom templates to a manually labeled "gold standard."
> >> Does that sound reasonable? Do you have any other suggestions?
> >>
> >> Best,
> >> Jason
> >>
> >> --
> >> Jason A. Tourville, Ph.D.
> >> Research Assistant Professor
> >> Department of Speech, Language,
> >> and Hearing Sciences
> >> Boston University
> >> 677 Beacon St.
> >> Boston, MA 02215
> >> Phone: (617)353-9484
> >> Fax: (617)353-7755
> >>
> >>
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> >
> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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--
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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