I am finding something peculiar when looking at foci. To illustrate, I
created a smaller file with only one study (foci file attached). I went
through the following steps:

1. Opened PALS_B12.BOTH.TEMPLATE-Map_STEREOTAXIC-FOCI.73730.spec from the
2. Opened the foci file test1study.foci
3. Projected the foci using Layers/Foci/Project Foci to PALS atlas
(selecting 'project above surface [0.00]).

The projected foci can be viewed in the attached figure coordinates.jpg

Now I click on foci, and look the Identify Window. I find that for some, the
values in 'Original Sterotaxic Positions' match the coordinates in the foci
file. But for some (e.g., the one marked with a red ellipse in the figure) I
get one of the coordinates set to zero. For example for this focus, I get:

Focus 6: MolholmEtAl05.pitch  Class: pitch
     Original Stereotaxic Position (AFNI): 41.0 0.0 6.0
     Stereotaxic Position (FLIRT):  41.0 0.9 2.1

But focus 6 coordinates as specified in the foci file are 
actually [41, -75, 6]

The same happens to a few others (but not all) foci. Sometimes it is the y
coordinate that becomes zero, and sometimes the x coordinate. 

I verified that it is not something to do with the foci projection - the
same results are obtained if I click the foci before projection. 

Any idea what I may be doing wrong, or not interpreting correctly?



-----Original Message-----
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 08, 2006 7:49 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

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?
> Or do I have to go through some intermediate of transforming from one
> 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:

> Thanks,
> Leon   
> -----Original Message-----
> [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:
> 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
>> ------------------------------------------------------------------------
>> [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 
>> <http://pissaro.soc.huji.ac.il/%7Eleon/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.)

caret-users mailing list

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