Hi Alex, Would you mind creating a zip file of your spec file and its contents (including CSV) and uploading it here:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi If you are viewing at least one of those fiducial surfaces in the main window and you have at least one focus in that stereotaxic space, and it's near/above the cortex, then you should see the focus. If you don't, then here's another thing to try: Toolbar: D/C: Page selection surface miscellaneous: drawing mode hide surface. This will show foci obscured (under) the surface. If you still see no foci, check for a foci menu on the D/C page selection menu. Makee sure Foci Main show foci is turned on (don't think this is the problem). If you don't see a foci menu, then the foci failed to load. Donna On 04/01/2009 07:50 AM, Alex Fornito wrote: > 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 >> > > _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
