I was thinking, I often have a directory with output files from a bunch of participants in standard space, but no anatomical underlay. So I made an alias that will link in a template. But ideally, there would be some way in the AFNI controller to specify that instead of a file in the current directory, I would like one of the templates in the main AFNI directory as my underlay.
Anyway, it’s not urgent or necessary, and I don’t know if it would be useful to anyone else, but I thought I’d mention it.
Step 1: create a directory, say $HOME/aglobal
Step 2: copy any file(s) you want to be always present into that directory, for example, MNI152_2009_template.nii.gz
Step 3: in your $HOME/.afnirc file, add the line (to the ***ENVIRONMENT section)
AFNI_GLOBAL_SESSION = /Users/rwcox/aglobal
When you start AFNI, the files in this global session will always appear in the dataset choosers at the end. I personally use this “trick” to put the MNI nonlinear template (mentioned in Step 2) as a universal underlay.
Thanks Bob. To be honest, I intended to add to that post that there was probably a way to do it in AFNI that I was just unaware of, but then I forgot to write that. It certainly didn’t come as a surprise that AFNI was one step ahead of me.
In any case, since we’re on a roll here, there is one other thing I was wondering about. It would be great to have a way to automatically mask the overlay on the basis of the underlay. As things stand, if I run a second-level analysis I wind up making two copies, one of the original analysis and one masked by the intersection mask of the normalized data of the participants. But I don’t really need both these files. Ideally, there would be some way that the AFNI viewer could on-the-fly mask the overlay by something like the 3dAutomasked underlay resampled into the grid of the overlay. That way I could see all the blobs outside of the brain but if I wanted to not see them I could also do that, without making a new masked output file on disk (not that this is a big deal from a storage standpoint, it’s just an extra step that I have to do for every analysis).
Anyway, maybe there is a way to do something like this that I am unaware of, but in any case I thought I’d mention it. Thanks a lot either way.
Right-click on the “intensity bar” just to the right of the image. You’ll get a popup menu.
The item labeled “Automask?” is a toggle (on/off) switch that restricts the overlay display to the 2D automask generated from the current underlay image. This feature is (at least) approximately what you want.
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