Ps. In case this helps any: This is the wrong characther: '-', and this is
the right one: '-' . Using abs('-') in Matlab, the wrong one translates to
8211, while the correct minus sign translates to 45.  

-----Original Message-----
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 22, 2006 4:19 PM
To: Leon Deouell
Cc: 'Caret, SureFit,and SuMS software users'
Subject: Re: [caret-users] using caret for a meta-analysis

Hi Leon,

This looks like a bug to me.  I was able to replicate this behavior on 
my Caret 5.502 12/15/2006 Caret running RHEL.  The ID readout for these 
foci were just fine (readout followed by corresponding line from foci file):

Focus 2: MolholmEtAl05.pitch   Class: pitch
    Original Stereotaxic Position (AFNI): (42.0, 2.0, 53.0)
2,42,2,53,,MolholmEtAl05.pitch,0,R middle frontal gyrus,,,,Pure,,pitch

Focus 3: MolholmEtAl05.pitch   Class: pitch
    Original Stereotaxic Position (AFNI): (52.0, 10.0, 18.0)
3,52,10,18,,MolholmEtAl05.pitch,0,R inferior frontal gyrus,,,,Pure,,pitch

But these foci had their x or y coordinate component zeroed out:

Focus 4: MolholmEtAl05.pitch   Class: pitch
    Original Stereotaxic Position (AFNI): (0.0, 23.0, 51.0)
4,20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrus,,,,Pure,,pitch
[Note from Donna: If left SFG, then wouldn't it be -20?)

Focus 5: MolholmEtAl05.pitch   Class: pitch
    Original Stereotaxic Position (AFNI): (53.0, 0.0, 45.0)
5,53,38,45,,MolholmEtAl05.pitch,0,R inferior parietal lobule,,,,Pure,,pitch

Focus 6: MolholmEtAl05.pitch   Class: pitch
    Original Stereotaxic Position (AFNI): (41.0, 0.0, 6.0)
6,41,75,6,,MolholmEtAl05.pitch,0,R middle occipital gyrus,,,,Pure,,pitch

On 12/22/2006 03:26 AM, Leon Deouell wrote:
> Hi,
>
> 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
> /CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ folder
> 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?
>
> Thanks,
>
> Leon
>
>
>
>
>
>
>
> -----Original Message-----
> From: [EMAIL PROTECTED]
> [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?
>>   
>>     
> 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] <mailto:[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 
>>> <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.)

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