Timing of motion based censoring with XCP + original TR indices for output time series

Summary of what happened:

Hi - I have two more general questions, but I’m providing my command below in case it’s relevant.

  1. I would like to retain the option to explore the effect of more stringent motion thresholds later on. If I disable motion censoring through the xcp command, is it equivalent to manually filter the frames after processing has completed using the framewise displacement in the motion.tsv file? It seems like this is not possible, because motion thresholding occurs early in denoising and then the missing frames are temporarily replaced with interpolated data.

  2. Is there some part of the XCP output that lists the indices of the original TR for each row in the processed time series? For example, if there are 100 TRs total, but 40 of them are censored, how do I know which TRs the other 60 correspond to?

Thank you very much for your help!


Command used (and if a helper script was used, a link to the helper script or the command generated):

set -euxo pipefail

export FREESURFER_HOME=/Applications/freesurfer/7.2.0
export HOME_DIR=/Volumes/Seagate/

docker run --rm -it \
   -v ${HOME_DIR}BIDS/derivatives:/fmriprep:ro \
   -v ${HOME_DIR}work_xcp:/work:rw \
   -v ${HOME_DIR}BIDS/derivatives/xcp_d:/out:rw \
   -v ${FREESURFER_HOME}/license.txt:/out/fs_license:rw \
   pennlinc/xcp_d:latest \
   /fmriprep /out participant \
   --despike -w /work --smoothing 6 --fs-license-file /out/fs_license --mem-gb 15 --low-mem```



Environment (Docker, Singularity / Apptainer, custom installation):


@Steven, any chance you’d be able to help with this? Thanks so much!


Hi @ejcorn,

It is hard to prescribe an exact solution without knowing what your analysis goals are. But perhaps if you disable censoring and interpolation in XCP (--fd-thresh 0) and remove volumes differentially after XCP completes, you can best test the impact of different motion thresholds.

Not that I know of.


Thanks Steven, that’s very helpful. Appreciate it!