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

[jessica]

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

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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