[caret-users] Viewing multiple functional maps

[David Van Essen]

Alex, Stephanie, et al.,

1) Stephanie's RGB suggestion provides one excellent option for you  
to check out.

2) Another set of options is to use the Surface: ROI window, which  
allows you flexibility in selecting various regions using data in a  
metric column.  Then use the Surface ROI: Operate on Selected Nodes  
menu to draw borders around the ROI or to assign the ROI to an  
existing or new paint column.

3) If you'd like to have side-by-side viewing of different metric  
columns in different windows (which is quite handy for a lot of  
purposes), then do the following:
i) Make multiple copies of the coord file for the surface  
configuration you want to view (e.g., save the very inflated coord  
file with  'copy2' and 'copy3' inserted into the file name.
ii) view a separate copy of the desired configuration in each Caret  
window.
iii) In the Page Selection: Metric Selection window, use the Surface  
Coloration Applies To: pulldown menu to assign a different metric  
column to each coord file.  Up to 10 different columns can then be  
viewed concurrently in this way, and similar options are available  
for surface-shape and paint files/columns.

You can use the node ID option to highlight locations of interest  
that show up in all windows.

4) If you use any of these approaches and get displays that you find  
useful and want to return to in the future, don't forget to generate  
a 'scene' and save the scene file.  This can save huge amounts of  
time in later stages of analysis and in preparing and revising figures.

5) Finally, regarding documentation, there are a number of Caret- 
related resources that provide help with questions like this.  Within  
Caret, the Menu: Help offers quick access to (i) 'Caret Help', which   
has extensive documentation and tutorials; (ii) Caret Tips; and  
(iii)  Search Caret Website, which provides a google-like search of  
online Caret resources.

If there are additional suggestions for analysis capabilities needed  
or improvements to the search and tutorial capabilities, let us know.

David

On Oct 21, 2007, at 12:28 AM, Stephane Jacobs wrote:

> Hi Alex,
>
> I've only work a little with Caret myself, so there might be a  
> better way... Anyway, you can convert metrics files to an RGB paint  
> file, using up to 3 contrasts of your metrics at a time. Just go in  
> Attributes/Metrics/Convert a Metrics file to RGB paint, or  
> something like that. Then you select each contrast you want to  
> display as red, blue and/or green, and the overlap will  
> automatically be coded depending on the primitive colors of the 2  
> (or 3) contrasts overlapping.
>
> Hope this helps,
>
> Stephane
>
> --
> Stephane Jacobs
> Human Neuroimaging and Transcranial Stimulation Lab
> 36 Straub Hall, 1227 University of Oregon
> Eugene, OR 97403 - USA
> Email: sjacobs at uoregon.edu
> Tel: (1) 541-346-4184
>
> On Sun, 21 Oct 2007 10:56:08 +1000 (EST), Alexander Fornito  
> <fornitoa at unimelb.edu.au> wrote:
>> Hi all,
>> Is there anyway to view more than one functional map (i.e., stat  
>> image) on
>> the PALS atlas simultaneously?
>> I have mapped the results of a series of contrasts onto the atlas  
>> and now
>> have a .metric file with each contrast as a different column.  
>> However, I
>> only seem to be able to view one contrast at a time.
>> I can't seem to find any documentation on this.
>> Ultimately, I would like to overlay two maps simultaneously (each  
>> coloured
>> using a different palette).
>> Also, if it is possible to view >1 map at the same time, is there  
>> some
>> option to colour areas of overlap between the maps differently?
>> Thanks for your help,
>> Alex
>>
>>
>>
>> Alex Fornito
>> JN Peters Research Fellow
>> Melbourne Neuropsychiatry Centre
>> National Neuroscience Facility
>> The University of Melbourne
>> Levels 2 & 3, 161 Barry St
>> Carlton South 3053 Vic Australia
>> Ph:    +61 3 8344 1861
>> Fax:   +61 3 9348 0469
>> Email: fornitoa at unimelb.edu.au
>>
>>
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