Thanks again for your help. I am making nice progress. My questions now are: 1. Is it possible to see the foci on volume slices? It seems I can only see them on surface files. 2. Regardless of foci, when I switch to 'oblique' in a window displaying a volume, I loose the yoking option - clicking on the surface does not change the display in the volume window and vice versa. Is there a way to tilt the volume and remain "yoked"?
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.) _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
