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

[David Van Essen]

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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