Hello,

I have been pre-processing my data using FMRIPREP, which incorporates FSL's mcflirt for volume alignment rather than AFNI's volreg. As such, I can't use volreg's -1Dfile option to create the motion parameters. Foruntately, fmriprep provides a confounds.tsv file for each EPI run, which includes motion parameters. What I've done is concatenate all the confounds.tsv files into one, removed the headers, and selected only the motion parameter columns (6 in total, where the translations are in mm, but rotations are in radians).

Next I generate the censor files:
1d_tool.py \
-infile $data_dir/$s/fmriprep/sub-${s}/func/sub-${s}_MoPar_all.1D \
-derivative \
-collapse_cols euclidean_norm \
-moderate_mask -1.0 1.0 \
-show_censor_count \
-write_censor $data_dir/$s/fmriprep/sub-${s}/func/sub-${s}.censor1.0mm_all.1D \
-write_CENSORTR $data_dir/$s/fmriprep/sub-${s}/func/sub-${s}.censorTR1.0mm_all.1D


Would this be an appropriate way to generate censor files (if some of the pre-processing isn't done with AFNI tools) in order to be used in 3dDeconvolve with the -censor option?

Thank you.