3dTproject input files for -ort option

AFNI Message Board
1

Hello —

It’s my first time working on the resting state data, and I would like to ask about which file to use as the ort input.
To note this first, I’m not using afni_proc.py (sorry!) and using the output from fmriprep and have deobliqued and blurred the data as a preprocessing step.

I put my motion parameters in a 1D file where each column has each parameter’s info, which I usually use in 3dDeconvolve. Can I use this 1D file directly in 3dTproject, or should I run 3dDeconvolve to create the x matrix (probably with x1D_stop option)?

I tried both and they appear similar but different — I would love to know which is recommended/what is the difference.

Also, should I detrend the data using 3dDetrend before using 3dTproject?

Thank you!
Yaelan

2

Hi Yaelan,

Have any trends already been projected, or any tedana regressors?

In general, provide -polort 0 and as many -ort and/or -dsort terms as you wish (where -ort files can have multiple columns). If no drifts have been projected already, then you might consider a -polort option that would be equivalent to that for 3dDeconvolve, i.e., 1+floor(run_length/150).

Detrending should be done in the same 3dTproject command, if it has not already been done. Actually, it should probably be done either way, since the motion terms might have trends in them.

  • rick
3

Awesome! I’ll then detrend it using the 3dTproject.
Thank you so much as always!