Hmmm... Now I'm a little confused. I actually can't see any little red dots. What I did was: 1. Open a spec file that has the coord files for the MRItotal, SPM99, SPM2, FLIRT and AFNI Fiducial surfaces (both left anf right, so 10 surfaces in total). 3.Create excel spreadsheet with study coords 4. Create study metadata file 5. Open coord file created in excel 6. Check the studies and foci are correctly linked (all seems ok, except I can't the studies in my metadata file in the 'studies' tabe of the map stereotaxic focus dialog) 7. Project foci to PALS atlas (seems to work ok)
After doing this, I can't see any red dots. Am I missing something? Do I have the wrong surfaces loaded perhaps? Also, I tried the colour creating command you suggested but got the following error COMMAND FAILED ERROR: Unrecognized operation: -color-file-create-missing-colors Not sure if this is because I might not have correctly-projected foci. Thanks again for your help, Alex On 01/04/2009 13:03, "David Van Essen" <vanes...@brainvis.wustl.edu> wrote: > Alex, > > Layers>Foci>Edit Foci Colors is one option for generating colors, but > it is indeed tedious if you have more than a few to assign. > > A better way is to capitalize on a color-creation option that John > recently implemented in Window -> Caret Command Executor. > Select COLOR FILE CREATE MISSING COLORS, then follow the instructions > in the Command Description box. This tells you how to enter input and > output color file names and specify the data file name and format > (foci or foci projection in your case). > > Once the quasi-random colors are assigned based on the foci names, you > may edit selected ones at your leisure if you don't like the > particular assignments. > > One other point - you should always be able to see the foci as little > red dots even if there are no foci colors assigned. If you saw > absolutely nothing, and if it is an unprojected foci file, you need to > view the fiducial surface. > > David > > > On Apr 1, 2009, at 4:54 AM, Alex Fornito wrote: > >> 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 > > _______________________________________________ > 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
