[caret-users] Quick projection of foci?
Alex Fornito
af397 at cam.ac.uk
Wed Apr 1 09:19:50 CDT 2009
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" <vanessen at 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" <vanessen at 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" <john at 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
>>>>> john at 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" <donna at 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 at 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: af397 at 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: fornitoa at unimelb.edu.au
>>>>>> Phone: +61 3 8344 1861
>>>>>> Fax: +61 3 9348 0469
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> caret-users mailing list
>>>>>> caret-users at brainvis.wustl.edu
>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> caret-users mailing list
>>>>> caret-users at 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: af397 at 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: fornitoa at unimelb.edu.au
>>>> Phone: +61 3 8344 1861
>>>> Fax: +61 3 9348 0469
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> caret-users mailing list
>>>> caret-users at brainvis.wustl.edu
>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>
>>> _______________________________________________
>>> caret-users mailing list
>>> caret-users at 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: af397 at 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: fornitoa at unimelb.edu.au
>> Phone: +61 3 8344 1861
>> Fax: +61 3 9348 0469
>>
>>
>>
>> _______________________________________________
>> caret-users mailing list
>> caret-users at brainvis.wustl.edu
>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
> _______________________________________________
> caret-users mailing list
> caret-users at 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: af397 at 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: fornitoa at unimelb.edu.au
Phone: +61 3 8344 1861
Fax: +61 3 9348 0469
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