Hi Remya,

Click Toolbar: D/C and select Surface Miscellaneous from the pull-down
menu at the top.  Select the checkbox labeled show cartesian axes.  I
confess I don't have Caret installed at home, where I'm answering, so I
can't be sure of the exact label.

Donna

> 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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