Hi Peter,
>
> Oddly specific enquiry: Is it possible to create a
> surface ROI (e.g. lh.xxx.niml.roi) from a surface
> dataset (e.g. lh.data.niml.dset) the same way you
> would use 3dcalc to generate a binary mask in
> volume space? In other words, is it possible to
> generate a surface ROI automatically, instead of
> drawing it, or somehow convert a surface dataset
> to an ROI? I understand that I can use 3calc to
> generate a binary mask surface dataset, but what
> if I want to actually make an ROI?
Well, the answer is yes and not quite. What do you mean by wanting to actualy make an ROI? Do you mean that you want a file that contains at each line a node index followed by an integer ID? Something like:
12 5
21 5
22 5
34 6
37 6
...
or do you want the result to be a bonified SUMA ROI file, something you can load back into the DrawROI interface and edit it complete with saved ROI drawing steps? The answer is yes-ish to the former, and no to the latter.
You'll have to tell me more about how you plan on making these ROIs automatically though. For instance, 3dcalc does not read surfaces so you can't use it to create datasets with node values determined based on node coordinates. But there are ways to trick these programs to do what you want them to, but doing so requires detailing how you plan on creating these ROIs.
>
> Also, unrelated, if I have made a SUMA color map
> like so:
>
MakeColorMap -fn fiducials.txt -suma_cmap
> my_colors.niml.cmap
> How do I make it so that it will show up among my
> colormap choices everytime I run SUMA on my
> machine?
This one's easy: the environment variable SUMA_CmapsDir is exactly what you need. If there is no entry for in your ~/.sumarc file, then it is high time for an env update with this command : suma -update_env . That command will preserve your current settings and add all new available env. variables.
cheers,
Ziad
>
> Best,
>
> Peter Kohler
