Hi John, Thanks so much for preparing the guide. I was able to follow the instructions and all seemed to work fine, except that when I re-load the foci into Caret after preparing the .csv file in excel, I get a message telling me that the foci file requires foci colours, but none have been loaded. I tried to create some colours using Layers>Foci>Edit Foci Colors, but I'm not sure how to assign the colours to different studies or foci classes. Consequently, I can't see any foci after they have been projected. Thanks again for your help, Alex
On 30/03/2009 20:25, "John Harwell" <j...@brainvis.wustl.edu> wrote: > 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 I think the format you are trying to use is out of date.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_fo >>> rm >>> 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 -- 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
