Dear Donna,
Thanks to your critical eye, I found out what the problem is. You noted that
for focus 4 the description is L Superior Frontal Gyrus but the x coordinate
was 20 in your readout. However, in the foci file I've sent, the line
actually says:
4,-20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrus,,,,Pure,,pitch
I am not sure what you used to read the foci file, but it seems this
software, like CARET, ignored the minus sign, and it turns out that all the
numbers which were zeroed in CARET, where actually negative numbers in my
original foci file. I tracked the problem back to the character used for the
minus sign. When I created the excel file (from which I created the CSV foci
file), I have sometimes cut and paste from PDF files or HTML files of the
original articles. In some cases, the minus sign was a longer dash sign
rather than a real minus sign. They look very similar but the wrong
character is a slightly longer line if you look at it carefully. If you open
the foci file I've sent before with Notepad (that is, if you use Windows)
you will see what I mean. When I replaced these characters with real minus
signs, the apparent bug was solved.
I think this is a point to keep in mind because I am pretty sure many would
cut and paste when creating large meta-analysis files (I have more than 100
points in the full file) rather than retype (which is also more prone to
errors). Maybe CARET can be configured to detect this somehow and either
report the problem or accept this other dash sign as minus.
Many thanks for the quick response.
Leon
-----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>
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