ROI selection and Colour bar colours

[Davide]

Hi,

Thanks for your great work with XjView, it is a very intuitive software!

I wonder if (and eventually how) I can do the following things:

- define the colours of the colour bar;

- load a ROI. I saw that I can select an overlay, which is great, but that changes the colours of the activation map and does not really hide activation clusters outside of the ROI (it just makes them light grey).

Any chance I can do these things?

Best,

Davide

[Xiaowei Song]

Yes, I think you can change the colorbar to any color mapping by directly modifying the code of xjview.m.

For example, in the 9.7 version of xjView.m, modifying the following line should do the trick:

7388th line: handles.colormap = colormap;

Or another trick would be to create your own colormap.m in current MATLAB path to intercept MATLAB's original colormap command.

For your 2nd question, my understanding is that you want use the "ROI" as a mask to remove all voxels outside of the ROI? Am I right? If this is the case, you might be able to do this with many ways. Such as using AFNI's 3dcalc: 3dcalc -a yourResult.nii -b mask.nii -expr "a*step(b)" -prefix maskedResult.nii .

Best,

Xiaowei

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Best,

Xiaowei Song