[caret-users] Viewing multiple functional maps

Mon Oct 22 08:14:19 CDT 2007

Hi Alex,

Use Attributes: Area Colors to control the color mapping of paint 
files.  You can't use palette files for paint files, because paint is 
ROI/discrete/parcellation, while metric is scalar/continuous/gradated.

Depending on the metric/scalar data, sometimes you can 
sum/subtract/multiply/divide (Attributes: Metric: Math Ops) multiple 
metric files to convey the information you want to show, but such cases 
are the exceptions.

Donna

On 10/21/2007 06:49 PM, Alex Fornito wrote:
> Thanks David,
> Is it possible to use the same palettes for the paint files as for the 
> metrics? I don't seem to be able to find a way.
>
>
> On 22/10/2007, at 1:28 AM, David Van Essen wrote:
>
>> 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 <mailto: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 <mailto: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 <mailto:fornitoa at unimelb.edu.au>
>>>>
>>>>
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>
> Alex Fornito
> JN Peters Research Fellow
> Melbourne Neuropsychiatry Centre
> Department of Psychiatry 
> The University of Melbourne
>
> Melbourne Neuropsychiatry Centre
> National Neuroscience Facility
> Levels 2 & 3, 161 Barry St
> Carlton South Vic 3053 Australia
>
> Phone: +61 3 8344 1861
> Fax: +61 3 9348 0469
> Email: fornitoa at unimelb.edu.au <mailto:fornitoa at unimelb.edu.au>
>
> www.psychiatry.unimelb.edu.au/mnc
>
>
>
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