Instacorr not displaying properly

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1

Hi. I am quite new to Afni, and I am using for the first time instacorr. I have a resting state processing output (called "errts.ct05_REML+tlrc"), inside the ct05.results folder. All the datasets result from an afni proc script that performed the standard steps for resting state processing (the REML method was used for regression).

I tried to follow the steps shown in 31 - Resting State & InstaCorr: Part 2 of 2 | The Center for Brains, Minds & Machines by R. Reynolds to setup the instacorr analysis in the GUI. I set the errts as dataset to use, turned off bandpass, turned on automask and use SeedRadius of 4 mm. After a while, the GUI flags "ready" in Instacorr options.

However, nothing happens when I try "Instacorr Set" on any point of the underlay (anatomical, epi or anything I tried, all registered to the MNI152 template). Moreover, if I try to manually switch on the "see Overlay" option, the GUI loads and displays a random other dataset from the results folder, always ignoring the instacorr setup.

What am I doing wrong?

Thanks in advance

AFNI version info (afni -ver): AFNI_24.2.03 'Macrinus'

2

Hi-

When you have errts time series (which are "residuals" of modeling, and by definition should have mean=0), I don't think you will want to have automasking on. Automasking something with mean=0 can be tricky at best, if not fully deletorious to the outcome at worst. I would set automasking to off.

Note you can do the rightclick->"Instacorr Set" thing, but easier (and more fun!) should be to:

  • hold down Ctrl+Shift
  • left-click anywhere in the brain

That should be enough to see full patterns. You will see the patterns throughout the whole FOV, not just within a brain mask, but that can also be pretty informative and useful.
NB: I find it helpful to underlay an antomical, so the data are resampled to the underlay grid for a bit, and then to turn on the "alpha thresholding" (transparent thresholding) and "box outlining" (threshold boundary visualization) via the "A" and "B" buttons. The benefits of this are described here:

Note that you should be able to fire up the APQC HTML with an interactive server running, and click the "IC" (=InstaCorr) buttons by images, as described in detail here:

... and more briefly here:

The above requires having Flask and Flask-Cors, as described in the miniconda install instructions here. Though, you don't need to use Miniconda to get those, just noting that specifically in case you are already using that.

Please let us know if that is still not working.

--pt

3

That worked perfectly. The main problem was in automask.
Thank you very much for the reply and the information for the usage of instacorr.
Ms

4

Cool, glad that sorted it out. It is definitely something that I forget from time to time, too, and so it causes some confusion.

--pt