Summary of what happened
Hello everyone,
I’m new to the community and have a couple of questions about fMRIPrep, specifically regarding native space analysis.
To potentially improve statistical power, I want to perform my analysis in native space on a dataset of 32 subjects. I’m using fMRIPrep with the --output-spaces func
argument to customize the space. However, I notice that the confounds files are not being generated.
Am I missing something in the setup, or is this an expected behavior when using only the --output-spaces func
flag?
Additionally, I was expecting the T1w scans would be coregistered to native space, but I only see the desc-preproc_T1w.nii.gz
and corresponding .json
file. Do I need to provide additional arguments for T1w-to-native space coregistration, or is this transformation not performed by fMRIPrep, meaning I should use ANTs or another tool for this purpose?
Any guidance would be appreciated!
Thank you for the help in advance.
Command Used
apptainer run \
--cleanenv \
--containall \
--bind ${FMRIPREP_RESOURCES_PATH}:/resources \
--bind ${BIDS_DIR}:/data \
--bind ${WORK_DIR}:/work \
--home ${OUTPUT_DIR}:/output \
--env TEMPLATEFLOW_HOME=/resources/templateflow \
${FMRIPREP_RESOURCES_PATH}/fmriprep.sif /data /output \
participant --participant_label $PARTICIPANT_LABEL \
--nprocs 8 \
--mem 8000 \
--skip-bids-validation \
--output-spaces func \
-w /work \
--debug all \
--fs-license-file /resources/license.txt \
--bids-filter-file /resources/bids_filter_file.json \
Version:
23.2.0
Environment (Docker, Singularity / Apptainer, custom installation):
Apptainer
Data formatted according to a validatable standard? Please provide the output of the validator:
Skipping the BIDS validation.