I’m working on a morphological study (cortical thickness, etc) with a longitudinal dataset where each subject contains 6 scan sessions. Using fMRIPrep version 23.2.1
(via Apptainer), I used the following command:
"unset PYTHONPATH; apptainer run \
-B ${bids_root_dir}:${bids_root_dir} \
-B ${templateflow_home_dir}:/opt/templateflow \
-B ${work_dir}:${work_dir} \
${bids_root_dir}/derivatives/fmriprep-${fmriprep_version}.simg \
$bids_root_dir $output_dir \
participant \
--participant-label $s \
--skip-bids-validation \
--md-only-boilerplate \
--anat-only \
--longitudinal \
--fs-license-file $FREESURFER_HOME/license.txt \
--output-spaces fsaverage fsLR \
--nthreads $cores \
--stop-on-first-crash \
--resource-monitor \
--mem_mb $reduced_mem \
--use-plugin $bids_root_dir/fmriprep_plugin_${s}.yml \
--verbose \
--output-layout bids \
-w $work_dir/sub-${s}"
This provides an unbiased anatomical template in my subject’s output anat
folder; however, within the subject’s session anat folders there is only a transform file *from-orig_to-T1w_mode-image_xfm.txt
.
I’m a bit unsure how to proceed. Given the longitudinal nature of this dataset, I need to compare morphological measures across subjects’ scan sessions, yet fMRIPrep only generates a single template. My initial thought was to use --bids-filter-file
to specify a specific session T1w; however, I worry this is excessive, as for each subject I’d have 6 separate jobs.