3dTproject question

AFNI Message Board
1

Hello,
I recently ran afni_proc.py to pre-process my data. Because I wanted to run ICA-fix, I used the pb02 image output for those analyses. Then, I wanted to regress out motion and bandpass the ICA-fixed data (the image that I used as the input). In order to do this, I decided to run 3dTproject. Is this the appropriate step for me to take? Below is the 3dTproject command I used:

3dTproject -polort 1 –input /$BaseDirHC/${i}/${i}.feat/filtered_func_data_clean.nii.gz
-censor /$BaseDirHC/${i}/${i}.feat/SUBJ${i}.results/censor_SUBJ${i}_combined_2.1D -cenmode ZERO
-ort /$BaseDirHC/${i}/${i}.feat/SUBJ${i}.results/X.nocensor.xmat.1D -prefix errts.subj${i}.tproject

Thank you!

2

Hello,

While I am not familiar with the details of ICA-fix, it is
supposed to remove unwanted signals. And so it would seem a
bit strange to still regress out motion terms and bandpass
afterwards. Using up degrees of freedom should be a big
question here. How many terms were removed via ICA-fix?
And to run 3dTproject properly, those removed terms should
be passed to it as an additional -ort term.

Regardless of using afni_proc.py or 3dTproject, this step
should be verified with with the authors of ICA-fix. Do
they intend or allow for that subsequent cleaning?

Ignoring all of that, I assume that the X.nocensor.xmat.1D
file was created via afni_proc.py with the -regress_bandpass
option. So that part looks reasonable.

But it would be more comforting if you could additionally
pass the terms removed by ICA-fix, and make sure that is an
operation they find reasonable.

  • rick