Hi Moran,
I suggest that you take further FreeSurfer specific questions to the FS
list. But to briefly answer your question, even though the surfaces and
stats are computed in the subject's native space, you still want to
include the talairach stage because it is used "behind the scenes" as
part of other stages and to derive an estimate of intracranial volume.
cheers,
-MH
On Wed, 2012-02-01 at 18:19 +0200, Moran Artzi wrote:
> Hi,
>
> Regarding to cortical thickness calculation using FreeSurfer (in
> subject space)
>
> The first step of the analysis, -autorecon1, includes Talairach
> transform computation which is not suitable for our data set.
>
> How can I run this analysis without this phase?
>
>
>
> Thanks a lot in advance for your time and your help in this issue
>
> Moran
>
>
>
> On Wed, Feb 1, 2012 at 6:06 PM, Moran Artzi <[log in to unmask]> wrote:
> Thanks
> Moran
>
>
> On Wed, Feb 1, 2012 at 3:05 PM, Bruce Fischl
> <[log in to unmask]> wrote:
> Hi Moran
> The thickness calculations are always performed in
> subject space, not standard space.
> Cheers
> Bruce
>
>
>
> On Feb 1, 2012, at 1:32 AM, Moran Artzi
> <[log in to unmask]> wrote:
>
> > Dear Experts
> > We are studying brains of subjects with substantial
> brain malformation.
> > Is it possible to calculate cortical thickness in
> FreeSurfer without transferring the data into standard
> space?
> > Otherwise Is there an alternative tool to study
> cortex thickness in the subject space?
> >
> > Thanks a lot
> > Moran
> >
> >
>
>
> 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.
>
>
>
>
|