@grayplot

AFNI Message Board
1

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

2

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

3

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

4

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

5

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

6

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.

7

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).

8

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

Look for version AFNI_18.2.10.

  • rick