Is there a clever way of separating out stimulus and baseline subbricks?

AFNI Message Board
1

Hello,

I was wanting to calculate percent change per voxel, but I was wondering if there is a clever way of separating out the stimulus and baseline subbricks in a block design? I know I can do this by 3dtcat, but I was wondering if there is a way of doing this automatically based on the reference function? My task has some pseudo random ordering in it and I was hoping I could separate things without having to do it by hand for every data set.

Appreciate any thoughts.

Thanks.

2

HI Leo,

If you view this in terms of when the expected BOLD
response is non-zero, then it would be simple to do,
grabbing the volumes when the ideal time series is
non-zero, e.g. (in tcsh syntax) for some ideal_TASK.1D:

set task_vols = `1d_tool.py -show_trs_uncensored encoded -infile ideal_TASK.1D`
3dTcat -prefix data_TASK all_runs+tlrc"[$task_vols]"
  • rick
3

I get this error message:

** FATAL ERROR: can’t decipher index codes from …/…/TC_D2+orig[]

This looks like looking for the on blocks. Is there a similar way to do the opposite? From the point of view that the offs would be zeros that is.

4

It is hard to say much without seeing your commands.
Are you running tcsh or bash?

And what happens with that 1d_tool.py command alone?
Get that to work correctly before grabbing the output.

  • rick
5

Ah, I think I’m running bash. I’m working on a supercomputing node. I’m not sure if I can switch to tcsh…

I’ll pull up a VM and try it there.

The output of the 1d_tool.py looks like this: 32…45,98…111,186…195
It looks like it is working fine to me.

6

So in bash syntax that might be:

task_vols=$(1d_tool.py -show_trs_uncensored encoded -infile ideal_TASK.1D)
  • rick