Alex Open the color file in caret after it is created David Sent from my iPhone
On Apr 1, 2009, at 9:19 AM, Alex Fornito <af...@cam.ac.uk> wrote: > 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 _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
