That seems to do the trick. Thanks. -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David Vanessen Sent: Sunday, January 07, 2007 7:30 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] using caret for a meta-analysis
Leon, I can replicate and explain your observations in the following way: 1) Load a foci file that contains data in multiple stereotaxic spaces, and view the foci with the FLIRT average fiducial surface in the main window.. At this stage, each focus will be in its original space, even though you are viewing the FLIRT average fiducial surface. 2) Open a second Caret window that contains a non-fiducial surface (e.g., the inflated surface). Note that no foci are visible on the inflated surface prior to projection. 3) Apply Layers: Foci: Project Foci to PALS atlas. As the projection process occurs, each focus that didn't start out as already being in FLIRT space will jump to a new position, by an amount that reflects the difference between FLIRT and whatever space the focus originated in. Concurrently, foci will start appearing on the inflated surface. Once the projection process is completed, each focus should be visible only once on the fiducial surface. 4) Open the original foci file (using Open File or using Toolbar: Spec) and Append it to the current foci. Now you should see most (but perhaps not all) foci doubled in the average fiducial surface view but not in the inflated view. In other words, I infer that you inadvertently loaded both the foci and the foci projection file to create the view in your email. In general, you will want to avoid such quasi-duplication. Instead, only view foci projection data once the projection is complete, unless you have a specific need to see the foci in their original space. I hope this resolves your question. David On Jan 7, 2007, at 3:37 AM, Leon Deouell wrote: > Hi, > > I am displaying my foci now(post projection to PALS-B12) on the > FIDUCIAL > Human.PALS_B12.LEFT_AVG_B1-12.FIDICUAL_FLIRT.clean.73730.coord. For > some > reason, it looks like every blob is doubled (see window capture > attached). > I don't see this if I display the same foci on the inflated or > hyperinflated > brains. Any idea why this is happening? > > Thanks, > > Leon > > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Donna > Dierker > Sent: Friday, December 22, 2006 5:17 PM > To: Caret, SureFit, and SuMS software users > Subject: Re: [caret-users] using caret for a meta-analysis > > Thank YOU for figuring out your own problem -- a pretty obscure > one, at > that. > > I agree both minus and long dash should read as minus; I hope it's not > tough for John to do. Sometimes the I/O stuff is QT's domain and > not so > easy to control. > > On 12/22/2006 09:05 AM, Leon Deouell wrote: >> 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> >>>>> >>>>> > ---------------------------------------------------------------------- > -- >>>>> >>>>> _______________________________________________ >>>>> 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 > <capture.jpg> > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://pulvinar.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
