Ok , so its all done now and I see perfect overlap between the fiducial surface and volume after converting to the new stereotaxic space.
Thanks Donna and John for your prompt replies!!

Remya


On Mar 16, 2007, at 9:43 AM, John Harwell wrote:

Hi Remya,

Load both your volume and one fiducial surface and display the volume. On the Display Control's Overlay/Underlay Volume page, press the Settings tab. In the "Surface Outline" group, check the box in the row "Active Fiducial Surface" and you will see an outline of the surface where it intersects the currently displayed volume slice. If both your volume and surface are in the same stereotaxic space, you will see an image similar to that below.

<pastedGraphic.tiff>

----------------------------------------------------------
John Harwell
[EMAIL PROTECTED]
314-362-3467

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave.    Box 8108
St. Louis, MO 63110   USA

On Mar 15, 2007, at 4:36 PM, Remya Nair wrote:

Hi Donna,

Thank you for the very helpful reply. I have created the AC aligned volume and fiducial surfaces. Then, I changed the volume to show my inter-aural origin as desired by following your instructions and I have been able to do this successfully after a little bit of tweaking with the signs of the translation shifts. I also applied similar shifts to the fiducial surface but here I have a question. While in case of the volume it is easy to make out the new origin (R on the toolbar sets position to the new origin), how do I confirm the same in case of the fiducial surface. I am a little confused as to this. Is there a way to check this?

Thanks for the help so far and looking forward to any suggestions!

Remya

On Mar 14, 2007, at 4:25 PM, Donna Dierker wrote:

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

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