Alex, I think the format you are trying to use is out of date. I have added some information about reading foci from a spreadsheet at http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Foci .
----------------------------------- John Harwell j...@brainvis.wustl.edu Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave Box 8108 Saint Louis, MO 63110 On Mar 30, 2009, at 8:30 AM, Alex Fornito wrote: > I have had a look at those tutorials, but I was hoping to bypass the > whole > meta-data entry. All other potential solutions do not seem to do the > trick. > I have noticed one thing though. In following the dated guide I > cited in my > first email, I read a csv spreadsheet containing the foci into Caret > that > had the following format: > > tag-version 1 > tag-number-of-cells 20 > tag-number-of-comments 3 > tag-BEGIN-DATA > 0 x y z Study1 0 > 1 x y z Study1 0 > 2 x y z Study2 1 > 3 x y z Study2 1 > ... > 0 SPM2 > 1 SPM99 > > In the Map Stereotaxic focus dialog, I then assigned the stereotaxic > space > in the 'Studies' dialog based on on the labelling at the bottom > (e.g., 0 = > SPM2, 1=SPM99). I cliked 'Apply' for each focus and then tried to > project > them using Project Foci to PALS atlas. > It seemed to progress to completion without errors, but I cannot > visualize > the foci. I've noticed however, that if I close Caret, re-open it > then try > Project Foci to PALS atlas again, it tells me that the foci do not > have an > associated stereotaxic space. I'm guessing there is something wrong > in the > way I'm assigning the space. > > > > On 30/03/2009 13:49, "Donna Dierker" <do...@brainvis.wustl.edu> wrote: > >> Hi Alex, >> >> That thread is pretty old, and David has been focusing (it pains me >> to >> gratify his penchant for bad puns) a lot of effort on this subject. >> >> Have you seen these tutorials: >> >> http://sumsdb.wustl.edu/sums/stereotaxictocaretfoci.do >> >> Three things come to mind: >> >> * On the D/C menu, make sure the foci radio button at the very >> bottom of >> the overlay/underlay - surface page (or Foci main page) is toggled >> on. >> >> * Make sure you have a focicolor file loaded >> (http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_form >> ats.html#fociColorFile) >> >> * Make sure the fiducial surface you have loaded in the main window >> is >> in the same stereotaxic space as the foci. >> >> David may chime in, but I'm not sure when he returns from Germany. >> >> Donna >> >> On 03/30/2009 07:01 AM, Alex Fornito wrote: >>> Hi, >>> I'm trying to project some foci onto the PALS surface to get a quick >>> impression of activation peak locations. I've glanced through the >>> tutorials >>> and they described a fairly labour-intensive process requiring the >>> entry of >>> lots of different data about each study. At this stage, I am not >>> planning on >>> doing a formal meta-analysis and would just like to get obtain >>> some quick >>> visualizations. To this end, I was hoping to import data from a >>> spreadsheet >>> for visualization. I followed the instructions posted on the >>> following >>> mailing list thread >>> >>> http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg00982.html >>> >>> But, after following the process, I cannot visualize the foci. >>> That is, >>> while Caret seems to read the data ok, and I can see the foci >>> details in the >>> D/C, I can't actually see them on the surface. >>> Is there perhaps some extra step that I have missed? >>> >>> Thanks for your help, >>> Alex >>> >>> >>> >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > -- > > Alex Fornito > CJ Martin Post-Doctoral Fellow > Brain Mapping Unit > Department of Psychiatry > University of Cambridge > Downing Site > Downing St, Cambridge > UK CB2 3EB > > Email: af...@cam.ac.uk > Phone: +44 (0) 1223 764670 > Fax: +44 (0) 1223 336581 > > Australian Details: > > Melbourne Neuropsychiatry Centre > National Neuroscience Facility > Levels 1 & 2, Alan Gilbert Building > 161 Barry St > Carlton South 3053 > Victoria, Australia > > Email: forni...@unimelb.edu.au > Phone: +61 3 8344 1861 > Fax: +61 3 9348 0469 > > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
