Re: [caret-users] Monkey Atlas and stereotaxic

2007-03-16 Thread Remya Nair
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.




--
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/

Re: [caret-users] Monkey Atlas and stereotaxic

2007-03-16 Thread John Harwell

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.


<>

--
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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Re: [caret-users] Monkey Atlas and stereotaxic

2007-03-16 Thread donna
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
>>
>> ___
>> caret-users mailing list
>> caret-users@brainvis.wustl.edu
>> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>
>
> ___
> caret-users mailing list
> caret-users@brainvis.wustl.edu
> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>



Antw: Re: [caret-users] Monkey Atlas and stereotaxic

2007-03-15 Thread Freimut Juengling
Guten Tag
Die von Ihnen angeschriebene Person ist unter dieser eMail-Adresse nicht mehr 
erreichbar.

Wir danken für Ihre Kenntnisnahme.
Inselspital Bern*



Re: [caret-users] Monkey Atlas and stereotaxic

2007-03-15 Thread Remya Nair

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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Re: [caret-users] Monkey Atlas and stereotaxic

2007-03-14 Thread Donna Dierker

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




[caret-users] Monkey Atlas and stereotaxic

2007-03-14 Thread Remya Nair

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






Re: [caret-users] Monkey atlas and stereotaxic coordinates

2005-06-21 Thread Donna Hanlon

Hi Jochen,

Yes -- sometimes the right sign is counter-intuitive.

I'll add the generation of an interaural fiducial to my growing queue of 
atlas updates.


Donna

On 06/21/2005 02:25 PM, Jochen Ditterich wrote:

Thanks, Donna. I had to get the signs right, but it seems to be 
working now. The correct offsets are 0, +19, and +5.5. I would be 
happy to share the files if anybody is interested.


Best,

Jochen.

Donna Hanlon wrote:


Hi Dr. Ditterich,

No, I don't think you're doing anything wrong.  I think the problem 
is that we need a fiducial coord file that is aligned to the 
inter-aural axis, but we only have a AC-origin fiducial coord file.  
I'm guessing you're using this archive:


http://sumsdb.wustl.edu:8081/sums/archivelist.do?id=684673

You can try creating one yourself and see if it works.  Here are the 
origins of the volumes:


Macaque.F99UA1.LR.Brain.AC_origin.04-01-29+orig.HEAD
35.5 54.5 -30
Macaque.F99UA1.LR.Brain.InterAural_origin.04-01-29+orig.HEAD
35.5 35.5 -24.5

Take the difference and use the Surface: Transform menu to translate 
the AC-origin fiducial by the difference.  Then Save Data File: 
Coordinate File and name it differently, to reflect the inter-aural 
alignment.  It's worth a shot.


Donna

On 06/20/2005 12:49 PM, Jochen Ditterich wrote:


Hi!

I have a question regarding Caret and the monkey atlas. There are 4 
different files under "Volume Files - Anatomy". Two of them are 
apparently AC aligned, the two others are aligned with respect to 
the inter-aural axis. I would like to use the latter ones since this 
is the stereotaxic coordinate system we are working with. However, 
there seems to be a misalignment between the surface viewer and the 
volume viewer whenever I load one of the InterAural_aligned files. 
The correspondence seems to be OK whenever I load one of the 
AC_aligned files. Am I doing something wrong?


Thanks,

Jochen.

-

Jochen Ditterich, Ph.D.
Assistant Professor
Center for Neuroscience
University of California
1544 Newton Court
Davis, CA 95616
USA

office: +1 (530) 754-5084
lab:+1 (530) 754-6987
fax:+1 (530) 757-8827
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Re: [caret-users] Monkey atlas and stereotaxic coordinates

2005-06-21 Thread Jochen Ditterich
Thanks, Donna. I had to get the signs right, but it seems to be working 
now. The correct offsets are 0, +19, and +5.5. I would be happy to share 
the files if anybody is interested.


Best,

Jochen.

Donna Hanlon wrote:

Hi Dr. Ditterich,

No, I don't think you're doing anything wrong.  I think the problem is 
that we need a fiducial coord file that is aligned to the inter-aural 
axis, but we only have a AC-origin fiducial coord file.  I'm guessing 
you're using this archive:


http://sumsdb.wustl.edu:8081/sums/archivelist.do?id=684673

You can try creating one yourself and see if it works.  Here are the 
origins of the volumes:


Macaque.F99UA1.LR.Brain.AC_origin.04-01-29+orig.HEAD
35.5 54.5 -30
Macaque.F99UA1.LR.Brain.InterAural_origin.04-01-29+orig.HEAD
35.5 35.5 -24.5

Take the difference and use the Surface: Transform menu to translate the 
AC-origin fiducial by the difference.  Then Save Data File: Coordinate 
File and name it differently, to reflect the inter-aural alignment.  
It's worth a shot.


Donna

On 06/20/2005 12:49 PM, Jochen Ditterich wrote:


Hi!

I have a question regarding Caret and the monkey atlas. There are 4 
different files under "Volume Files - Anatomy". Two of them are 
apparently AC aligned, the two others are aligned with respect to the 
inter-aural axis. I would like to use the latter ones since this is 
the stereotaxic coordinate system we are working with. However, there 
seems to be a misalignment between the surface viewer and the volume 
viewer whenever I load one of the InterAural_aligned files. The 
correspondence seems to be OK whenever I load one of the AC_aligned 
files. Am I doing something wrong?


Thanks,

Jochen.

-

Jochen Ditterich, Ph.D.
Assistant Professor
Center for Neuroscience
University of California
1544 Newton Court
Davis, CA 95616
USA

office: +1 (530) 754-5084
lab:+1 (530) 754-6987
fax:+1 (530) 757-8827
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--

-

Jochen Ditterich, Ph.D.
Assistant Professor
Center for Neuroscience
University of California
1544 Newton Court
Davis, CA 95616
USA

office: +1 (530) 754-5084
lab:+1 (530) 754-6987
fax:+1 (530) 757-8827


Re: [caret-users] Monkey atlas and stereotaxic coordinates

2005-06-20 Thread Donna Hanlon

Hi Dr. Ditterich,

No, I don't think you're doing anything wrong.  I think the problem is 
that we need a fiducial coord file that is aligned to the inter-aural 
axis, but we only have a AC-origin fiducial coord file.  I'm guessing 
you're using this archive:


http://sumsdb.wustl.edu:8081/sums/archivelist.do?id=684673

You can try creating one yourself and see if it works.  Here are the 
origins of the volumes:


Macaque.F99UA1.LR.Brain.AC_origin.04-01-29+orig.HEAD
35.5 54.5 -30
Macaque.F99UA1.LR.Brain.InterAural_origin.04-01-29+orig.HEAD
35.5 35.5 -24.5

Take the difference and use the Surface: Transform menu to translate the 
AC-origin fiducial by the difference.  Then Save Data File: Coordinate 
File and name it differently, to reflect the inter-aural alignment.  
It's worth a shot.


Donna

On 06/20/2005 12:49 PM, Jochen Ditterich wrote:


Hi!

I have a question regarding Caret and the monkey atlas. There are 4 
different files under "Volume Files - Anatomy". Two of them are 
apparently AC aligned, the two others are aligned with respect to the 
inter-aural axis. I would like to use the latter ones since this is 
the stereotaxic coordinate system we are working with. However, there 
seems to be a misalignment between the surface viewer and the volume 
viewer whenever I load one of the InterAural_aligned files. The 
correspondence seems to be OK whenever I load one of the AC_aligned 
files. Am I doing something wrong?


Thanks,

Jochen.

-

Jochen Ditterich, Ph.D.
Assistant Professor
Center for Neuroscience
University of California
1544 Newton Court
Davis, CA 95616
USA

office: +1 (530) 754-5084
lab:+1 (530) 754-6987
fax:+1 (530) 757-8827
___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users





[caret-users] Monkey atlas and stereotaxic coordinates

2005-06-20 Thread Jochen Ditterich

Hi!

I have a question regarding Caret and the monkey atlas. There are 4 
different files under "Volume Files - Anatomy". Two of them are 
apparently AC aligned, the two others are aligned with respect to the 
inter-aural axis. I would like to use the latter ones since this is the 
stereotaxic coordinate system we are working with. However, there seems 
to be a misalignment between the surface viewer and the volume viewer 
whenever I load one of the InterAural_aligned files. The correspondence 
seems to be OK whenever I load one of the AC_aligned files. Am I doing 
something wrong?


Thanks,

Jochen.

-

Jochen Ditterich, Ph.D.
Assistant Professor
Center for Neuroscience
University of California
1544 Newton Court
Davis, CA 95616
USA

office: +1 (530) 754-5084
lab:+1 (530) 754-6987
fax:+1 (530) 757-8827