Hi Remya,
Glad to hear you got your hands on a T1 scan.
There's no documentation I know of that covers what you want to do, but
it's not that hard (if I understand it correctly).
I think you'll just need two versions of your volumes (one AC-centered,
one inter-aural) and two versions of your fiducial surface (ditto).
You'll need the AC-centered volume to create your fiducial surface,
which also will be AC-centered. When you're happy with your AC-centered
surface, then translate both volume and surface back to inter-aural.
The hard part is calculating the x,y,z translation offsets between the
AC-centered origin and your inter-aural origin. Sometimes it takes a
sign flip or two to get it right, but only you can compute the magnitude
of these shifts. I'll call them shiftx, shifty, shiftz.
Change your volume back to inter-aural like so:
Volume: Edit volume attributes: coordinates: origin: Adjust x,y,z by
shiftx,shifty,shiftz. After applying change, hit toolbar: R (with
volume view in main window) to reset the volume to the new origin, to
make sure it's correct. This may take trial and error to get the sign
right.
Once the volume view accurately reflects the inter-aural origin, save
the translated volume: File: Save Data File: volume files: NIFTI (or
AFNI or SPM/MedX, which is basically Analyze): my_interaural.nii
Now, translate your surface:
* switch to fiducial view in main window
* Window: Transformation matrix editor
* Translate: enter shiftx, shifty, shiftz (again -- sign-flipping as needed)
* Apply matrix to main window
In this case, if you get it wrong, then you'll need to use Toolbar: spec
to reload the fiducial after each trial, to get back to the original AC
origin.
Once you get it right, use File: Save data file: coord file to save the
translated coord file as a name like my.fiducial.inter-aural.coord.
Good luck.
Donna
On 03/14/2007 02:44 PM, Remya Nair wrote:
Hi Caret-Gods...!
I have a question regarding Caret and monkey atlas. I apologize for
the basic nature of these questions, but I am a newbie to Caret and
that is all i have to say in my defense!!!
We have T1 weighted 0.5 isotropic resolution anatomical images of
monkey brain. The final aim is to be able to reconstruct surfaces as
well as find the co-ordinates of points of interest w.r.t our
stereotaxic coord system. We are working with the inter-aural
stereotaxic system.
Ideally, apart from viewing the surface , we will need stereotaxic
coordinates to know exactly where the AP0 is, mediolateral coordinates
etc.
I have ,as per the Caret segmentation tutorial, segmented the volume
and created the surfaces. But, the way i have done it, the volume has
been centered at the AC (as per the tutorial instructions). What
should I do to center it to the inter-aural origin? is there any caret
documentation on this... if yes, could you please point me to them?
Consequently what would be the next steps I should perform (perhaps
registration?) to be able to read off the stereo-coords of interest as
per my coordinate system? Please do point me to the appropriate
tutorials/spec files that i may need.
Thanks in advance!!
RN
