Question
Hello - I just want to confirm that I am interpreting the xcp_d documentation correctly with regards to motion censoring in abcd mode. It seems like censoring is performed during preprocessing, and interpolated volumes are used when necessary. Then, the output time series contains interpolated volumes to retain the original dimensionality of the data, but it is up to the user to censor those interpolated volume based on the motion threshold (framewise displacement <0.3 by default) for their specific application. The create-matrices option generates correlation matrices using censored data.
The reason I want to confirm is that I have many volumes with fd >0.3 but the outliers.tsv files are all 0. Does the outliers file have no utility in abcd mode, and I should rely on manual thresholding of framewise displacement from motion.tsv in accordance with my chosen threshold?
Please let me know if I am missing something and thank you for your time!
Command used (and if a helper script was used, a link to the helper script or the command generated):
#!/bin/bash
set -euxo pipefail
export FREESURFER_HOME=/Applications/freesurfer/7.2.0
export HOME_DIR=/Volumes/Seagate/
for SES in {1..10}; do
for RUN in {1..4}; do
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 \
-v ${HOME_DIR}BIDS/bids_filters/bids_filter_ses${SES}_run${RUN}.json:/out/bids_filter.json:rw \
pennlinc/xcp_d:latest \
/fmriprep /out participant \
-w /work --fs-license-file /out/fs_license --mem-gb 15 --low-mem \
--bids-filter-file /out/bids_filter.json \
--participant_label AEON101 \
--mode abcd \
--smoothing 6 \
--combine-runs n \
--create-matrices all \
--motion-filter-type lp --band-stop-min 6 \
--file-format nifti \
--warp-surfaces-native2std n \
--min-time 0 \
--abcc-qc n
done
done
Version:
0.10.1
Environment (Docker, Singularity / Apptainer, custom installation):
docker