[caret-users] Quick projection of foci?

[John Harwell]

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I think the format you are trying to use is out of date.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/file_form
>> 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
>>>
>>>
>>>
>>
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>
> -- 
>
> 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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