Ok, I downloaded the newest version of Caret and I can see the foci now. The color file create missing colors does not seem to work though. If I enter the either the .foci or foci.proj file as the data file, it tells me that it is successful, but the foci do not change colours.
I can however change the colours through the map stereotaxic focus dialog, although this seems to be based on study name rather than class (?) On 01/04/2009 14:00, "David Van Essen" <vanes...@brainvis.wustl.edu> wrote: > Alex, > > 1) Did you turn on the foci view in Display Control -> Foci Main? > > 2) What version of Caret are you using? I think it needs to be Caret > 5.61. > > If this doesn't solve it, John will need to chime in as I'm off to a > meeting all day. > > David > > On Apr 1, 2009, at 7:50 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/fil >>>>>>> e_ >>>>>>> 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.htm>>>>>>>> l >>>>>>>> >>>>>>>> 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 > > _______________________________________________ > 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
