yes, it does exist in that space. As long as your folding pattern atlas is
in register with fsaverage it should work ok. But of course if your
motivation is that your pediatric subjects have different folding patterns
(which I'm not sure I believe unless they are *very* young), then the whole
p
I don't think this makes sense unless you have created a new label atlas
for your individual subjects. The current label atlas exists in the
fsaverage space. Maybe Bruce can weigh in.
On 03/05/2015 04:46 PM, Jason Tourville wrote:
> Hi Doug,
> Perhaps I should back up and explain our goal. We a
Hi Doug,
Perhaps I should back up and explain our goal. We are using Freesurfer to
recon pediatric data sets and are planning to use the surface labels as
seeds for connectivity studies and for morphometric analyses. We're
concerned that using the fsaverage surface template as the target for
surfac
The mris_register command is what does the registration and creates a
new sphere.reg file. surfreg just implements that command mris_register
command.
I'm not sure what you mean by the labeling steps.
On 03/05/2015 03:53 PM, Jason Tourville wrote:
> Hi Doug,
> I've run the steps outlined in th
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.r
Hi Bruce,
By template here, I mean the folding pattern .tif files. The intention is
to have a replacement for the fsaverage template for surfer
co-registration.
Cheers,
Jason
On Thu, Mar 5, 2015 at 3:18 PM, Bruce Fischl
wrote:
> Hi Jason
>
> I don't think so - you'll probably have to edit the
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 p
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 surf
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
