At the risk of stating the obvious, do you realise your FSL results are
/not/ in "Talairach space"? The ...2standard.mat transformations are to
MNI "standard" space, i.e., "almost Talairach". To do a Talairaching,
you must find some control points manually on your T1 image and (have
AFNI) calculate the transformation. This is what Darren's (interesting)
trick allows you to do once and for all, and use thereafter for all FSL
analyses. There have been some discussions about these different types
of "Talairach spaces", on this list and, no doubt, numerous others...
Christopher Bailey <[log in to unmask]>
PET Centre and
Center for Functionally Integrative Neuroscience
Aarhus University Hospital, Denmark
On Mon, 2004-11-22 at 07:27, Darren Schreiber wrote:
> What I have done is take advantage of these options with my FSL data in
> AFNI is to use an anatomical MNI space brain that has been marked in
> AFNI to allow it to be warped into Talairach space. So, in my
> directories, I have the following files:
> This allows AFNI to easily move my functional and anatomical data that
> I got from FSL output into the Talairach space and take advantage of
> AFNI's features.
> On Nov 21, 2004, at 9:08 PM, Jia Liu wrote:
> > Dear Mark -
> > Thanks for your prompt response, and sorry that I did not mention the
> > reason
> > in my previous email. I want to use AFNI TTatlas+tlrc Dataset as a
> > reference
> > to understand the anatomical location of the activation of my data
> > processed
> > by FSL (i.e. to use "Talairach to", "Where Am I", and "Atlas Colors"
> > feature
> > in AFNI). To do this, I guess I need to use Talairach View in the AFNI,
> > don't I? Thanks again for your help!
> > Best Regards!
> > Jia
> >> I'm also afraid that I don't know the status of Talairach
> >> coordinate viewing in AFNI for Analyze images. You can get
> >> coordinates in FSL by using FSLView or img2talcoord but I'm
> >> afraid they are the only options.
> >> All the best,
> >> Mark
> >> On 20 Nov 2004, at 05:34, Jia Liu wrote:
> >>> Dear all,
> >>> I am new to FSL, and have several rudimentary questions (I searched
> >>> both FSL
> >>> and ANFI website and their mailing lists, but failed to find the
> >>> answer).
> >>> 2) AFNI visualization
> >>> After processing data with FSL (ver 3.2) and creating links with
> >>> feat2afni,
> >>> AFNI (ver 2.56f) is able to display both anatomical (e.g. hires.hdr)
> >>> and
> >>> functional (e.g. example_func.hdr) data properly. However, the
> >>> Talairach
> >>> View option is disabled, but the transformation matrix is stored in
> >>> reg
> >>> folder (e.g. example_func2highres.xfm). Is there any way to load this
> >>> transformation matrix in AFNI? Or did I missed any step?
> >>> Thanks a lot!
> >>> Jia