I have FMRI data, and was wondering how to show more than one "ideal time series" at a time?
--pt
1 Like
Hello-
OK, I think the AFNI GUI can do that.
I'll use the Bootcamp data, from processing hte aud and vis task data in AFNI_data7/task_demo_ap, and using 2 ideal*.1D time series that are output in the *.results directory from running afni_proc.py. Each of these have 450 time points, and go with the datasets outputs in the regress block of AP processing.
In this case, I will load the fitts* dataset as the Underlay data, and open up a Graph window. In particular, I've jumped to this XYZ coordinate: -20 94 -4 (in the default RAI DICOM notation). The data looks like this:
The 2 ideal time series files I want to load are: ideal_aud.1D and ideal_vis.1D. In the lower right of the image window, I can click FIM -> Pick Ideal, and then choose one of these to load. If I pick ideal_aud.1D, The result looks like:
That's great, but I was both time series loaded!
As far as I can tell, the best way to do this is to:
- combine both ideal time series into a single file of multiple columns (here 2, because there are 2 files),
- explicitly tell AFNI to use different colors per line, because otherwise when I load the multi-column file the ideal time series will be the same red color and I won't be able to tell them apart.
To do the first job, I found it convenient to use the following terminal commands, to concatenate multiple column files, and also make sure they are each vertically aligned well:
paste ideal_aud.1D ideal_vis.1D | column -t > ideal_ALL.1D
This makes a new, multicolumn file called ideal_ALL.1D. The above works with any number of coluimn files. The first few lines can be displayed, looking like this (the second column should indeed start with all zeros here, so great):
$ head ideal_ALL.1D
0 0
0.0526548 0
0.37117 0
0.714956 0
0.900383 0
0.970763 0
0.992416 0
0.998211 0
0.999616 0
0.999932 0
To do the second job, you can use the AFNI environment variable AFNI_IDEAL_COLORS, whose description is:
AFNI_IDEAL_COLORS (editable)
This variable, if set, allows you to specify the set of colors used
for the FIM Ideal overlay in the graph viewer window. Separate color
names by colons, as in "red:green:blue". The first column in the
Ideal 1D file gets the first color; the second column gets the second
color, and so on. The variable AFNI_ORT_COLORS can similarly be used
to specify the colors for the FIM Ort overlay.
So, you could do one of the following to set it:
- in using a tcsh shell/script, I gave the environment variable (at least 2 colors here):
setenv AFNI_IDEAL_COLORS red:blue:green:violet:orange:rbgyr20_03 - in a bash terminal/script, you could run:
export AFNI_IDEAL_COLORS=red:blue:green:violet:orange:rbgyr20_03 - in your
~/.afnircfile, you could put this line:AFNI_IDEAL_COLORS = red:blue:green:violet:orange:rbgyr20_03
After doing one of those things, I fired up afni, chose the same underlay and location, and in the lower right of the Graph window selected FIM -> Pick Ideal -> ideal_ALL.1D. And I got this nice colorful image with my multiple ideal time series:
If my ideal had more columns, I would get lots of colors (here, I'm choosing a motion_demean.1D dataset, just to have something with 6 columns):
If my ideal had more columns than colors that I had provided, the last color will "stick" for columns that outnumber the number of colors.
Hope that is helpful!
--pt
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There is a simple way to show two (no more) 1D timeseries as color overlays in the graph window. Use the FIM menu button to 'Pick Ideal'. Then use 'Pick Ort' to choose a second file.
Now, the 'Ort' is shorthand for a nuisance time series regressor, not an ideal. For the purposes of looking at the curves, though, it doesn't matter what the function of the 'Ort' vs. 'Ideal' is -- you can see both of them this way.
2 Likes