@grayplot

Dear AFNI wizards,

I tried using @grayplot and was encountering errors (unable to read the directory), so I updated my afni binaries (Precompiled binary macos_10.12_local: Jul 31 2018 (Version AFNI_18.2.06)) and now the program @grayplot is gone. Is it really gone? Will it return one day?

Thank you,
Kate

Hi, Kate-

That is surely a quirky error on the part of our build process, and not a permanent change.

I have PMed you instructions to copy the most recent version of the code into a text file, make it executable, and then put it into your “~/abin/” directory (or wherever you have installed your AFNI binaries), and then you shoudl be good to go for now.

We will try to do a build in the near future to correct this in the distributed binaries. Thanks for bringing it to our attention.

–pt

Thanks Paul!

The code still created an error for me, and I realized it was because my data are in orig space, and @grayplot is hardcoded to expect +tlrc in the image files. So I changed that and the program worked–thank you again!

Best,
Kate

Hi, Kate-

OK, I asked The Bob a bit more about this program, and he mentioned that @grayplot script is specifically made to partner with afni_proc.py output-- for most applications, this means that the relevant files to plot will be *+tlrc.BRIK/HEAD files; there will also be other things present to add to the plots. To do this, the @grayplot script has some hardwired features (e.g., the “tlrc” space assumption).

If you just want to make grayplots of a given time series file in a more general context, you can go to the source program, 3dGrayplot, which @grayplot utilizes:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/programs/3dGrayplot_sphx.html#ahelp-3dgrayplot

One or the other might be easier for a given usage case.

–pt

Thanks Paul! Yea I was using it on the afni_proc.py output, but I don’t use the tlrc option in my scripts (I keep everything in native space for my analyses). I used the 3dGrayPlot program but I like that the @grayplot program plots the motion parameters and censored volumes.

Thanks again for making this program–very useful!

Best,
Kate

It did not occur to me to make @grayplot work with +orig space outputs in afni_proc.py

I will modify it to check what the final “space” is and adjust the filenames it looks for to match.
WHEN? Perhaps this weekend.

I have made the change to @grayplot so it will use +orig datasets if +tlrc datasets are not found.

This change will be in the next binary build. If you send me email to robertcox@mail.nih.gov then I can email you a copy of this script to use immediately, since I can’t predict when the next build will take place (a week, maybe).

A build was run yesterday, finishing around noon,
so Bob’s updates should be available.

Look for version AFNI_18.2.10.

  • rick