[caret-users] Foci uncertainty limits using RGB paint files; changing foci colors

[David Van Essen]

Jessica,

On Jan 21, 2008, at 2:30 PM, jessica wrote:

> Thanks again David...I've assigned classes in the ".foci"  
> sheet...one very very last question regarding your instructions here:
>
> "If you assign one set of foci a 'class' [e.g., motion] and another  
> set of foci a different class [e.g., color], and then assign a  
> distinct color to each class, you can view them in distinct colors  
> by selecting Coloring Mode: Focus Class in the Foci Main Page."
>
> How do I assign colors to classes?  Can I use the "Names" column in  
> the ".focicolor" sheet?

Yes, that is one way - just enter the class terms in addition to the  
study names.

>  Or do I need to go through a menu from the GUI?

In Caret, there is a Layers: Foci: Edit Foci Colors option, which  
brings up a fairly self-explanatory window for creating, editing, and  
deleting foci colors.  If you have a small number of classes, this may  
be easier, and in any event it allows for post hoc adjustment of the  
colors.

David
>
>
> thanks,
> jessica
>
>
> David Van Essen wrote:
>> Jessica,
>> Answers to both questions:
>> On Jan 21, 2008, at 10:04 AM, jessica f cantlon wrote:
>>> Thank you David...I started over and everything looks to be  
>>> working now.
>> Good!
>>>
>>> I was wondering if there is any info about how to estimate peaks  
>>> as spheres and then flatten them.  I saw an article that did  
>>> something to this effect (Lewis, J., 2006, Cortical networks  
>>> related to human use of tools, The Neuroscientist, 12(3), p.  
>>> 211).  However, I couldn't find any info on how to do this in the  
>>> tutorials.  Maybe there isn't anything in which case I can try to  
>>> figure something out myself.
>> The following steps may get you where you want to go.  (There's not  
>> a tutorial on this yet....)
>> Load the foci that you want 'painted' on the surface, and in the  
>> desired colors.
>> Keep the left and right hemisphere foci as separate foci projection  
>> files.
>>    [Notes:  (i) If they are currently combined, they can be  
>> separated by viewing the foci on just one hemisphere, then using  
>> the Foci: Delete Foci Not Displayed on Main Window Surface.  (ii)  
>> This can be a bit of a pain, so a future modification may allow  
>> concurrent projection to left and right hemispheres.]
>> Make sure that you have the appropriate PALS fiducial surface  
>> loaded.  If more than one is currently loaded, make sure the  
>> desired one is the 'active' fiducial surface using the Display  
>> Control: Surface Miscellaneous: Active Fiducial pulldown.
>> Select Layers: Foci: Convert Uncertainty Limits to RGBpaint.
>> Choose the distances you want for lower, middle, and upper limits.   
>> The default (upper limit = 10, the others = 0) is a good starting  
>> point.
>> Give the RGB Paint column name an appropriate header.
>> Press ok.  It may take a few minutes if you have lots of foci.
>> View your results by choosing RGB Paint as a primary or secondary  
>> overlay in the Display Control page.
>> Save the RGB paint file if you like it.  You can create multiple  
>> columns in a single file.
>> On Jan 21, 2008, at 1:06 PM, jessica f cantlon wrote:
>>> Hi David,
>>>
>>> Sorry for inundating you with questions.  I was wondering if it is  
>>> possible to have one study colored with two different colors  
>>> depending on the condition.  I am trying to show all of one kind  
>>> of effect in one color and all of another kind in another color  
>>> but sometimes both of these kinds of effects come from one study.   
>>> Is it possible to do this?
>> Yes, indeed, by using the 'focus class' option.
>> If you assign one set of foci a 'class' [e.g., motion] and another  
>> set of foci a different class [e.g., color], and then assign a  
>> distinct color to each class, you can view them in distinct colors  
>> by selecting Coloring Mode: Focus Class in the Foci Main Page.
>> To make the class assignments, you can either paste them in the  
>> Class column when generating the initial (or revised) spreadsheet  
>> (the fastest way) or you can enter the class one focus at a time  
>> using the Layers: Foci: Map Stereotaxic Focus option.  For the  
>> latter, press 'Edit Number', then increment each number after  
>> entering the Class.  IMPORTANTLY, you have to press the Apply  
>> button after each entry in order to save it; if you don't want to  
>> reproject the foci while you're making these entries, DE-SELECT the  
>> 'automatic projection of foci' button at the top.
>>>
>>> thanks again,
>>> jessica
>>>
>>> p.s. I would spend more time to figure this stuff out myself but  
>>> we are doing a TICS paper that is due in a couple of weeks and I  
>>> want to use some figures like these.
>> I hope this works for you; I'd be interested in seeing a preprint  
>> (or at least the relevant figures) at some point in the future.
>> David VE
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