Re: [caret-users] using caret for a meta-analysis

[Donna Dierker]

On 12/08/2006 11:44 AM, Leon Deouell wrote:

Dear Donna,

Thanks for the information. I realize the issue of different coordinate
spaces. What I am not sure of is this: If I specify the original space
(e.g., T88 or SPM2) for each study in the foci text file, or in the study
tab when entering individual foci using the GUI (5.2.2 in the tutorial),
will Caret take this into consideration when projecting to the PALS brain?
  

Yes

Or do I have to go through some intermediate of transforming from one space
to another? Originally I was considering using the tal2mni Matlab function
from the Cambridge imagers web site you mentioned to get all coordinates
into MNI space, but maybe this is redundant in Caret.
  
The idea is to make this unnecessary -- as long as the stereotaxic space 
in question is well-represented by one of these:


711-2C
AFNI
FLIRT
MRITOTAL
SPM2
SPM95
SPM96
SPM99

Thanks,

Leon   


-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 08, 2006 6:34 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

Hi Leon,

Shawn has done exactly what you want to do, so if anyone knows the 
pitfalls, he does. ;-)


Besides Shawn's useful notes, make sure you read sections 1.2.3 and 5.2 
of this tutorial, if you haven't done so already:


CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6585200

This tutorial includes a spec file intended for this purpose. The ones 
in the Caret fmri_mapping directory are not really intended for use as 
"visualization" specs; rather, Caret uses them when mapping fMRI data 
onto PALS_B12. You can, however, use the average fiducial surfaces in 
that directory for your foci-related purposes. Note that studies report 
results in stereotactic spaces other than MNI (e.g., AFNI users report 
true Talairach-Tournoux (T88) coordinates, which differs significantly 
from MNI -- see http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach; 
wustl.edu researchers typically use "711-2*" space -- somewhere between 
T88 and MNI). See 
http://brainvis.wustl.edu/help/pals_volume_normalization/ for additional 
details.


Reading tutorial section 5.2 may clarify some of this, but you're likely 
to have residual questions/confusion about these spaces.


On 12/08/2006 10:24 AM, Christ, Shawn E. wrote:
  

Hi Leon,

I have been working with David, Donna, and John on utilizing Caret for 
precisely this purpose with respect to an ALE-type meta-analysis on 
deception that we have submitted for publication. You can download a 
copy of our spec file, etc. at 
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996


I've also uploaded a copy of my personal notes on how to transform 
foci using Caret. They can be found at 
http://www.shawnchrist.com/FociTransform.pdf


I hope this helps!

Best,

-Shawn

--

Shawn Christ, Ph.D.

Assistant Professor

Department of Psychological Sciences

University of Missouri-Columbia

210 McAlester Hall

Columbia, MO 65211

[EMAIL PROTECTED] 



*From:* [EMAIL PROTECTED] 
[mailto:[EMAIL PROTECTED] *On Behalf Of *Leon 
Deouell

*Sent:* Friday, December 08, 2006 9:50 AM
*To:* caret-users@brainvis.wustl.edu
*Subject:* [caret-users] using caret for a meta-analysis

Hi,

I am in the process of doing a meta-analysis of imaging data. I am a 
complete novice to Caret, but from a quick look it seems it's 
stereotaxic foci functions would be ideal to log the peak activity 
data from different studies. Eventually I would like to display 
symbols for each peak on a 3D brain rendering of some sort. Perhaps 
Naively, I thought I could load a template brain (open a spec file), 
add foci (assuming for a moment I have all coordinates in MNI space) 
using for example 'layers>foci>map stererotaxic focus', and see them 
pop-out on the brain. However, at first pass, I run into the following 
questions:


a) What brain (spec file) should I load from the fMRI_mapping folder? 
There are so many of them. Is there anywhere a text file describing 
what these different files are?


b) If I enter a focus with coordinates which happen to be under the 
surface by a few millimeters, they don't show up on the surface. Is 
there a way to project them to the surface or to make the brain 
'transparent'?


c) Once I have the foci entered, can I project them to an inflated 
brain, and if so, how?


Finally, I assume I am not the first to want to use Caret for this 
purpose - does someone have a 'recipe' for such a project or tips on 
what pitfalls to avoid?


Thanks,

Leon



Dr. Leon Y Deouell, MD, PhD

Department of Psychology

The Hebrew University of Jerusalem

Jerusalem 91905

Israel

Tel: +972-2-5881739

Fax: +972-2-5825659

http://pissaro.soc.huji.ac.il/~leon/Lab 

RE: [caret-users] using caret for a meta-analysis

[Leon Deouell]

Dear Donna,

Thanks for the information. I realize the issue of different coordinate
spaces. What I am not sure of is this: If I specify the original space
(e.g., T88 or SPM2) for each study in the foci text file, or in the study
tab when entering individual foci using the GUI (5.2.2 in the tutorial),
will Caret take this into consideration when projecting to the PALS brain?
Or do I have to go through some intermediate of transforming from one space
to another? Originally I was considering using the tal2mni Matlab function
from the Cambridge imagers web site you mentioned to get all coordinates
into MNI space, but maybe this is redundant in Caret.

Thanks,

Leon   

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 08, 2006 6:34 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

Hi Leon,

Shawn has done exactly what you want to do, so if anyone knows the 
pitfalls, he does. ;-)

Besides Shawn's useful notes, make sure you read sections 1.2.3 and 5.2 
of this tutorial, if you haven't done so already:

CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6585200

This tutorial includes a spec file intended for this purpose. The ones 
in the Caret fmri_mapping directory are not really intended for use as 
"visualization" specs; rather, Caret uses them when mapping fMRI data 
onto PALS_B12. You can, however, use the average fiducial surfaces in 
that directory for your foci-related purposes. Note that studies report 
results in stereotactic spaces other than MNI (e.g., AFNI users report 
true Talairach-Tournoux (T88) coordinates, which differs significantly 
from MNI -- see http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach; 
wustl.edu researchers typically use "711-2*" space -- somewhere between 
T88 and MNI). See 
http://brainvis.wustl.edu/help/pals_volume_normalization/ for additional 
details.

Reading tutorial section 5.2 may clarify some of this, but you're likely 
to have residual questions/confusion about these spaces.

On 12/08/2006 10:24 AM, Christ, Shawn E. wrote:
>
> Hi Leon,
>
> I have been working with David, Donna, and John on utilizing Caret for 
> precisely this purpose with respect to an ALE-type meta-analysis on 
> deception that we have submitted for publication. You can download a 
> copy of our spec file, etc. at 
> http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996
>
> I've also uploaded a copy of my personal notes on how to transform 
> foci using Caret. They can be found at 
> http://www.shawnchrist.com/FociTransform.pdf
>
> I hope this helps!
>
> Best,
>
> -Shawn
>
> --
>
> Shawn Christ, Ph.D.
>
> Assistant Professor
>
> Department of Psychological Sciences
>
> University of Missouri-Columbia
>
> 210 McAlester Hall
>
> Columbia, MO 65211
>
> [EMAIL PROTECTED] 
>
> 
>
> *From:* [EMAIL PROTECTED] 
> [mailto:[EMAIL PROTECTED] *On Behalf Of *Leon 
> Deouell
> *Sent:* Friday, December 08, 2006 9:50 AM
> *To:* caret-users@brainvis.wustl.edu
> *Subject:* [caret-users] using caret for a meta-analysis
>
> Hi,
>
> I am in the process of doing a meta-analysis of imaging data. I am a 
> complete novice to Caret, but from a quick look it seems it's 
> stereotaxic foci functions would be ideal to log the peak activity 
> data from different studies. Eventually I would like to display 
> symbols for each peak on a 3D brain rendering of some sort. Perhaps 
> Naively, I thought I could load a template brain (open a spec file), 
> add foci (assuming for a moment I have all coordinates in MNI space) 
> using for example 'layers>foci>map stererotaxic focus', and see them 
> pop-out on the brain. However, at first pass, I run into the following 
> questions:
>
> a) What brain (spec file) should I load from the fMRI_mapping folder? 
> There are so many of them. Is there anywhere a text file describing 
> what these different files are?
>
> b) If I enter a focus with coordinates which happen to be under the 
> surface by a few millimeters, they don't show up on the surface. Is 
> there a way to project them to the surface or to make the brain 
> 'transparent'?
>
> c) Once I have the foci entered, can I project them to an inflated 
> brain, and if so, how?
>
> Finally, I assume I am not the first to want to use Caret for this 
> purpose - does someone have a 'recipe' for such a project or tips on 
> what pitfalls to avoid?
>
> Thanks,
>
> Leon
>
> 
>
> Dr. Leon Y Deouell, MD, PhD
>
> Department of Psychology
>
> The Hebrew University of Jerusalem
>
> Jerusalem 91905
>
> Israel
>
> Tel: +972-2-5881739
>
> Fax: +972-2-5825659
>
> http://pissaro.soc.huji.ac.il/~leon/Lab 
> 
>
> -

Re: [caret-users] using caret for a meta-analysis

[Donna Dierker]

Hi Leon,

Shawn has done exactly what you want to do, so if anyone knows the 
pitfalls, he does. ;-)


Besides Shawn's useful notes, make sure you read sections 1.2.3 and 5.2 
of this tutorial, if you haven't done so already:


CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6585200

This tutorial includes a spec file intended for this purpose. The ones 
in the Caret fmri_mapping directory are not really intended for use as 
"visualization" specs; rather, Caret uses them when mapping fMRI data 
onto PALS_B12. You can, however, use the average fiducial surfaces in 
that directory for your foci-related purposes. Note that studies report 
results in stereotactic spaces other than MNI (e.g., AFNI users report 
true Talairach-Tournoux (T88) coordinates, which differs significantly 
from MNI -- see http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach; 
wustl.edu researchers typically use "711-2*" space -- somewhere between 
T88 and MNI). See 
http://brainvis.wustl.edu/help/pals_volume_normalization/ for additional 
details.


Reading tutorial section 5.2 may clarify some of this, but you're likely 
to have residual questions/confusion about these spaces.


On 12/08/2006 10:24 AM, Christ, Shawn E. wrote:


Hi Leon,

I have been working with David, Donna, and John on utilizing Caret for 
precisely this purpose with respect to an ALE-type meta-analysis on 
deception that we have submitted for publication. You can download a 
copy of our spec file, etc. at 
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996


I’ve also uploaded a copy of my personal notes on how to transform 
foci using Caret. They can be found at 
http://www.shawnchrist.com/FociTransform.pdf


I hope this helps!

Best,

-Shawn

--

Shawn Christ, Ph.D.

Assistant Professor

Department of Psychological Sciences

University of Missouri-Columbia

210 McAlester Hall

Columbia, MO 65211

[EMAIL PROTECTED] 



*From:* [EMAIL PROTECTED] 
[mailto:[EMAIL PROTECTED] *On Behalf Of *Leon 
Deouell

*Sent:* Friday, December 08, 2006 9:50 AM
*To:* caret-users@brainvis.wustl.edu
*Subject:* [caret-users] using caret for a meta-analysis

Hi,

I am in the process of doing a meta-analysis of imaging data. I am a 
complete novice to Caret, but from a quick look it seems it's 
stereotaxic foci functions would be ideal to log the peak activity 
data from different studies. Eventually I would like to display 
symbols for each peak on a 3D brain rendering of some sort. Perhaps 
Naively, I thought I could load a template brain (open a spec file), 
add foci (assuming for a moment I have all coordinates in MNI space) 
using for example 'layers>foci>map stererotaxic focus', and see them 
pop-out on the brain. However, at first pass, I run into the following 
questions:


a) What brain (spec file) should I load from the fMRI_mapping folder? 
There are so many of them. Is there anywhere a text file describing 
what these different files are?


b) If I enter a focus with coordinates which happen to be under the 
surface by a few millimeters, they don't show up on the surface. Is 
there a way to project them to the surface or to make the brain 
'transparent'?


c) Once I have the foci entered, can I project them to an inflated 
brain, and if so, how?


Finally, I assume I am not the first to want to use Caret for this 
purpose – does someone have a 'recipe' for such a project or tips on 
what pitfalls to avoid?


Thanks,

Leon



Dr. Leon Y Deouell, MD, PhD

Department of Psychology

The Hebrew University of Jerusalem

Jerusalem 91905

Israel

Tel: +972-2-5881739

Fax: +972-2-5825659

http://pissaro.soc.huji.ac.il/~leon/Lab 





___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
  



--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)

RE: [caret-users] using caret for a meta-analysis

[Leon Deouell]

Hi Shawn,

 

Just what I was hoping for. Many thanks. 

 

Best,

 

Leon

 

 

 

  _  

From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Christ, Shawn
E.
Sent: Friday, December 08, 2006 6:25 PM
To: caret-users@brainvis.wustl.edu
Subject: RE: [caret-users] using caret for a meta-analysis

 

Hi Leon,

 

I have been working with David, Donna, and John on utilizing Caret for
precisely this purpose with respect to an ALE-type meta-analysis on
deception that we have submitted for publication.  You can download a copy
of our spec file, etc. at
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996

 

I've also uploaded a copy of my personal notes on how to transform foci
using Caret.  They can be found at
http://www.shawnchrist.com/FociTransform.pdf

 

I hope this helps!

 

Best,

-Shawn

 

 

--

Shawn Christ, Ph.D.

Assistant Professor

Department of Psychological Sciences

University of Missouri-Columbia

210 McAlester Hall

Columbia, MO 65211

[EMAIL PROTECTED]

 

  _  

From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Leon Deouell
Sent: Friday, December 08, 2006 9:50 AM
To: caret-users@brainvis.wustl.edu
Subject: [caret-users] using caret for a meta-analysis

 

Hi,

I am in the process of doing a meta-analysis of imaging data. I am a
complete novice to Caret, but from a quick look it seems it's stereotaxic
foci functions would be ideal to log the peak activity data from different
studies. Eventually I would like to display symbols for each peak on a 3D
brain rendering of some sort. Perhaps Naively, I thought I could load a
template brain (open a spec file), add foci (assuming for a moment I have
all coordinates in MNI space) using for example 'layers>foci>map
stererotaxic focus', and see them pop-out on the brain. However, at first
pass, I run into the following questions:

a) What brain (spec file) should I load from the fMRI_mapping folder? There
are so many of them. Is there anywhere a text file describing what these
different files are?

b) If I enter a focus with coordinates which happen to be under the surface
by a few millimeters, they don't show up on the surface. Is there a way to
project them to the surface or to make the brain 'transparent'?

c) Once I have the foci entered, can I project them to an inflated brain,
and if so, how?

Finally, I assume I am not the first to want to use Caret for this purpose -
does someone have a 'recipe' for such a project or tips on what pitfalls to
avoid?

Thanks,

Leon



Dr. Leon Y Deouell, MD, PhD

Department of Psychology

The Hebrew University of Jerusalem

Jerusalem 91905

Israel

Tel: +972-2-5881739

Fax: +972-2-5825659

 http://pissaro.soc.huji.ac.il/~leon/Lab

RE: [caret-users] using caret for a meta-analysis

[Christ, Shawn E.]

Hi Leon,

 

I have been working with David, Donna, and John on utilizing Caret for
precisely this purpose with respect to an ALE-type meta-analysis on
deception that we have submitted for publication.  You can download a
copy of our spec file, etc. at
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996

 

I've also uploaded a copy of my personal notes on how to transform foci
using Caret.  They can be found at
http://www.shawnchrist.com/FociTransform.pdf

 

I hope this helps!

 

Best,

-Shawn

 

 

--

Shawn Christ, Ph.D.

Assistant Professor

Department of Psychological Sciences

University of Missouri-Columbia

210 McAlester Hall

Columbia, MO 65211

[EMAIL PROTECTED]

 



From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Leon
Deouell
Sent: Friday, December 08, 2006 9:50 AM
To: caret-users@brainvis.wustl.edu
Subject: [caret-users] using caret for a meta-analysis

 

Hi,

I am in the process of doing a meta-analysis of imaging data. I am a
complete novice to Caret, but from a quick look it seems it's
stereotaxic foci functions would be ideal to log the peak activity data
from different studies. Eventually I would like to display symbols for
each peak on a 3D brain rendering of some sort. Perhaps Naively, I
thought I could load a template brain (open a spec file), add foci
(assuming for a moment I have all coordinates in MNI space) using for
example 'layers>foci>map stererotaxic focus', and see them pop-out on
the brain. However, at first pass, I run into the following questions:

a) What brain (spec file) should I load from the fMRI_mapping folder?
There are so many of them. Is there anywhere a text file describing what
these different files are?

b) If I enter a focus with coordinates which happen to be under the
surface by a few millimeters, they don't show up on the surface. Is
there a way to project them to the surface or to make the brain
'transparent'?

c) Once I have the foci entered, can I project them to an inflated
brain, and if so, how?

Finally, I assume I am not the first to want to use Caret for this
purpose - does someone have a 'recipe' for such a project or tips on
what pitfalls to avoid?

Thanks,

Leon



Dr. Leon Y Deouell, MD, PhD

Department of Psychology

The Hebrew University of Jerusalem

Jerusalem 91905

Israel

Tel: +972-2-5881739

Fax: +972-2-5825659

 http://pissaro.soc.huji.ac.il/~leon/Lab

[caret-users] using caret for a meta-analysis

[Leon Deouell]

Hi,

I am in the process of doing a meta-analysis of imaging data. I am a
complete novice to Caret, but from a quick look it seems it's stereotaxic
foci functions would be ideal to log the peak activity data from different
studies. Eventually I would like to display symbols for each peak on a 3D
brain rendering of some sort. Perhaps Naively, I thought I could load a
template brain (open a spec file), add foci (assuming for a moment I have
all coordinates in MNI space) using for example 'layers>foci>map
stererotaxic focus', and see them pop-out on the brain. However, at first
pass, I run into the following questions:

a) What brain (spec file) should I load from the fMRI_mapping folder? There
are so many of them. Is there anywhere a text file describing what these
different files are?
b) If I enter a focus with coordinates which happen to be under the surface
by a few millimeters, they don't show up on the surface. Is there a way to
project them to the surface or to make the brain 'transparent'?
c) Once I have the foci entered, can I project them to an inflated brain,
and if so, how?

Finally, I assume I am not the first to want to use Caret for this purpose -
does someone have a 'recipe' for such a project or tips on what pitfalls to
avoid?

Thanks,

Leon


Dr. Leon Y Deouell, MD, PhD
Department of Psychology
The Hebrew University of Jerusalem
Jerusalem 91905
Israel

Tel: +972-2-5881739
Fax: +972-2-5825659

 http://pissaro.soc.huji.ac.il/~leon/Lab