Re: [Freesurfer] project locations from template to individual MRIs

On 03/11/2014 05:10 PM, peng wrote:

Hi Doug, With the terminology in the document you provided, I can summarize what I want to do exactly as part of the flow chart in page 7. I listed it as between==. As described in the document, I can get Ta, Tb by <mri_info –vox2ras-tkr vol>; and R from a file <register.dat>; am I right? Practically, I may put my template as a subject a0, and individuals as subjects a1, a2 ..., an. What is the file name of [Vol A TkReg "RAS"] under the subject folder?

That is not meant to be a volume, just the name of the space/coordinate system (distinguishes it from other spaces). doug

============== [Volume A CRS] -> (Ta) -> [Vol A TkReg "RAS"] <- (R) <- [ Vol B TkReg "RAS"] <- (Tb) <- [Volume B CRS] ============== Thanks a lot.

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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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422

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