what template? When discussing coordinate systems you have to be very specific. A template could be a volume template or a surface template. If a volume template it could be MNI305 or MNI152. If MNI152 it could be the 1mm version or the 2mm version. All of these things are important and the questions cannot be answered without these details. doug

On 03/11/2014 12:42 PM, peng wrote:

Thanks Doug, I will read the document. But may I ask a simpler question: in freesurfer, do you use affine transformation to make correspondence between a individual subject and the template (the procedure someone calls as normalization)?

best Peng

On Tue, Mar 11, 2014 at 5:06 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Hi Peng, there's a lot going on there, and it is not specific
enough for
me to make recommendations. Take a look at the docs we have on our
coordinate systems

http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.pdf

you might get the answer you need from there or at least use our
terminology to point me in the right direction

doug




On 03/10/2014 12:20 PM, peng wrote:
> Thanks Doug for your reply. In fact I need both. I do this
mainly for
> computation (in volume); and display (in surface) is also cool.
>
> The dots (e.g. A1, A2, ..., An, ..., AN) were originally defined in
> volume of the template (icbm152). This can be implemented as an Nx3
> matrix S, where S(n, :) = [nx, ny, nz] indicates the location of
An in
> the volume.
> RAS here I mean such a coordinate system that, [0 0 0] is AC and
the 3
> dimensions are taking right, anterior, superior as positive, e.g
> An([nx0 ny0 nz0]) indicates a location nx0 mm right, ny0 mm anterior
> and nz0 mm superior of AC.
> The above two systems can be easily transformed by a transformation
> matrix.
>
> I wish to know the correspondent locations of An in individual
> subject(B), as Bn. e.g. if A1 is center of V1 in the template, I
wish
> to find the center of V1 in the subject as B1.
> So far, all the locations are represented in volume. However, I
guess
> to normalise the individual brain to the template, freesurfer will
> extract the volumes to surfaces. I imagine the procedure will be
like
> An (volume representation of dots in template)  -> ASn (surface
> representation of dots in template) -> BSn(surface representation of
> dots in individual) -> Bn(volume representation of dots in
> individual). If this assumption is correct, I would like to use
Bn for
> my computation and ASn for display later.
>
> I hope I have made myself clearer.
>
> best
> Peng
>
>
> On Mon, Mar 10, 2014 at 4:21 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:
>
>
>     Do you mean you want to display them in the MRI volume or on the
>     surface
>     (or both)? When you say that they are in "RAS coordinates", what
>     do you
>     mean? How are the coords defined?
>     doug
>
>
>
>     On 03/08/2014 07:26 AM, peng wrote:
>     > Dear freesurfers,
>     >
>     >    I have a set of dot locations (300~400) in a template
brain,
>     > indicated by indices of a 3-D array of the template MRI
data, which
>     > can be easily transformed to RAS coordinates. I wish to
project
>     these
>     > dot locations to individual MRIs, ideally also as indicated by
>     indices
>     > in the 3-D array of the individual MRI data. Is it
possible to do it
>     > in freesurfer? I guess the surface-based procedure shall work
>     well for
>     > this. It might be a very junior question, if it was documented
>     > somewhere before, please let me know the link. Thank you very
>     much for
>     > help.
>     >
>     > best
>     > Peng
>     >
>     >
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