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+#!/bin/bash
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+#$ -N halfpipe
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+#$ -q compute7.q
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+#$ -j y
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+#$ -o halfpipe.log.txt
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+#$ -cwd
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+#$ -pe smp 2 -binding linear
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+#$ -l h_rt=48:0:0
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+#$ -l virtual_free=20480M
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+
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+#$ -t 101-10000
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+
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+set -e
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+set -x
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+
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+base_directory=/ifs/loni/faculty/njahansh/collaborators/lea/ukbiobank
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+clinical_directory=${base_directory}/clinical_data
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+
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+dataset_directory=$(mktemp -d)
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+bids_directory=$(mktemp -d)
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+synthseg_directory=$(mktemp -d)
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+halfpipe_directory=$(mktemp -d)
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+
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+synthseg_container=${base_directory}/synthseg.sif
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+halfpipe_container=${base_directory}/halfpipe-latest-240307.sif
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+
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+read -r -a files < <(sed -n "${SGE_TASK_ID}p" ${base_directory}/tasks.txt)
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+
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+for file in "${files[@]}"; do
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+ ln -s "${file}" "${dataset_directory}"
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+done
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+
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+mamba run --name clinica \
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+ clinica convert ukb-to-bids \
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+ "${dataset_directory}" \
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+ "${clinical_directory}" \
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+ "${bids_directory}"
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+
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+t1w_file=$(find "${bids_directory}" -name "*_T1w.nii.gz" -print -quit)
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+mv -v "${t1w_file}" "${synthseg_directory}/t1w.nii.gz"
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+
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+singularity run \
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+ --bind "${synthseg_directory}" \
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+ ${synthseg_container} \
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+ --i "${synthseg_directory}/t1w.nii.gz" \
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+ --o "${synthseg_directory}/synthseg.nii.gz" \
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+ --robust \
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+ --cpu --threads 1
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+
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+singularity exec \
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+ --bind "${synthseg_directory}" \
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+ ${halfpipe_container} \
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+ antsApplyTransforms \
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+ --dimensionality 3 \
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+ --input "${synthseg_directory}/synthseg.nii.gz" \
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+ --reference-image "${synthseg_directory}/t1w.nii.gz" \
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+ --output "${synthseg_directory}/synthseg_in_t1w_space.nii.gz" \
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+ --interpolation MultiLabel \
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+ --verbose
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+
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+singularity exec \
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+ --bind "${base_directory}" \
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+ --bind "${synthseg_directory}" \
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+ ${halfpipe_container} \
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+ ${base_directory}/apply_mask.py \
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+ "${synthseg_directory}/t1w.nii.gz" \
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+ "${synthseg_directory}/synthseg_in_t1w_space.nii.gz" \
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+ "${t1w_file}"
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+
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+cat <<EOF >"${halfpipe_directory}/spec.json"
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+{
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+ "halfpipe_version": "1.2.2.post1.dev535+gc31d205",
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+ "schema_version": "3.0",
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+ "timestamp": "2023-08-08_16-01",
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+ "global_settings": {
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+ "dummy_scans": 0,
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+ "slice_timing": true,
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+ "use_bbr": null,
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+ "skull_strip_algorithm": "none",
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+ "run_mriqc": false,
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+ "run_fmriprep": true,
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+ "run_halfpipe": true,
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+ "fd_thres": 0.5,
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+ "anat_only": false,
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+ "write_graph": false,
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+ "hires": false,
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+ "run_reconall": false,
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+ "t2s_coreg": false,
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+ "medial_surface_nan": false,
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+ "bold2t1w_dof": 9,
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+ "fmap_bspline": true,
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+ "force_syn": false,
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+ "longitudinal": false,
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+ "regressors_all_comps": false,
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+ "regressors_dvars_th": 1.5,
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+ "regressors_fd_th": 0.5,
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+ "skull_strip_fixed_seed": false,
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+ "skull_strip_template": "OASIS30ANTs",
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+ "aroma_err_on_warn": false,
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+ "aroma_melodic_dim": -200,
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+ "sloppy": false
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+ },
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+ "files": [
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+ {
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+ "metadata": {},
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+ "datatype": "bids",
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+ "path": "${bids_directory}"
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+ },
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+ {
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+ "suffix": "events",
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+ "path": "${bids_directory}/task-{task}_events.tsv",
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+ "extension": ".tsv",
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+ "datatype": "func"
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+ }
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+ ],
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+ "settings": [
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+ {
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+ "ica_aroma": true,
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+ "smoothing": {
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+ "fwhm": 6.0
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+ },
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+ "grand_mean_scaling": {
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+ "mean": 10000.0
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+ },
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+ "bandpass_filter": {
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+ "hp_width": 125.0,
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+ "lp_width": null,
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+ "type": "gaussian"
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+ },
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+ "name": "icaAromaSetting",
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+ "filters": [
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+ {
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+ "type": "tag",
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+ "action": "include",
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+ "values": [
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+ "facesshapesemotion"
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+ ],
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+ "entity": "task"
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+ }
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+ ],
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+ "output_image": false
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+ },
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+ {
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+ "ica_aroma": false,
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+ "smoothing": {
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+ "fwhm": 6.0
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+ },
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+ "grand_mean_scaling": {
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+ "mean": 10000.0
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+ },
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+ "bandpass_filter": {
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+ "hp_width": 125.0,
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+ "lp_width": null,
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+ "type": "gaussian"
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+ },
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+ "confounds_removal": [
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+ "(trans|rot)_[xyz]"
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+ ],
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+ "name": "motionParametersSetting",
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+ "filters": [
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+ {
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+ "type": "tag",
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+ "action": "include",
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+ "values": [
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+ "facesshapesemotion"
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+ ],
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+ "entity": "task"
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+ }
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+ ],
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+ "output_image": false
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+ },
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+ {
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+ "ica_aroma": false,
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+ "smoothing": {
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+ "fwhm": 6.0
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+ },
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+ "grand_mean_scaling": {
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+ "mean": 10000.0
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+ },
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+ "bandpass_filter": {
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+ "hp_width": 125.0,
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+ "lp_width": null,
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+ "type": "gaussian"
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+ },
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+ "name": "noConfoundsSetting",
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+ "filters": [
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+ {
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+ "type": "tag",
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+ "action": "include",
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+ "values": [
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+ "facesshapesemotion"
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+ ],
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+ "entity": "task"
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+ }
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+ ],
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+ "output_image": false
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+ }
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+ ],
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+ "features": [
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+ {
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+ "name": "icaAroma",
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+ "setting": "icaAromaSetting",
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+ "contrasts": [
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+ {
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+ "type": "t",
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+ "name": "faceNegVsControl",
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+ "values": {
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+ "Face": 1.0,
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+ "Shape": -1.0
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+ }
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+ }
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+ ],
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+ "hrf": "dgamma",
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+ "conditions": [
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+ "Face",
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+ "Shape"
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+ ],
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+ "type": "task_based",
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+ "high_pass_filter_cutoff": 125.0
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+ },
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+ {
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+ "name": "motionParameters",
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+ "setting": "motionParametersSetting",
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+ "contrasts": [
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+ {
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+ "type": "t",
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+ "name": "faceNegVsControl",
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+ "values": {
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+ "Face": 1.0,
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+ "Shape": -1.0
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+ }
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+ }
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+ ],
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+ "hrf": "dgamma",
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+ "conditions": [
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+ "Face",
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+ "Shape"
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+ ],
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+ "type": "task_based",
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+ "high_pass_filter_cutoff": 125.0
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+ },
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+ {
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+ "name": "noConfounds",
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+ "setting": "noConfoundsSetting",
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+ "contrasts": [
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+ {
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+ "type": "t",
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+ "name": "faceNegVsControl",
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+ "values": {
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+ "Face": 1.0,
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+ "Shape": -1.0
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+ }
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+ }
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+ ],
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+ "hrf": "dgamma",
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+ "conditions": [
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+ "Face",
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+ "Shape"
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+ ],
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+ "type": "task_based",
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+ "high_pass_filter_cutoff": 125.0
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+ }
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+ ],
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+ "models": []
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+}
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+EOF
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+
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+singularity run \
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+ --contain \
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+ --cleanenv \
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+ --bind /tmp \
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+ ${halfpipe_container} \
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+ --workdir "${halfpipe_directory}" \
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+ --skip-spec-ui \
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+ --nipype-n-procs "$(nproc)" \
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+ --keep none
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+
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+derivatives_directory=${halfpipe_directory}/derivatives
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+mask_file=$(find "${derivatives_directory}" -name "*_desc-brain_mask.nii.gz" \( -not -name "*space*" \) -print -quit)
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+report_file=$(find "${halfpipe_directory}/reports" -name "*_skull_strip_report*svg" -print -quit)
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+
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+singularity exec \
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+ --bind /tmp \
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+ ${halfpipe_container} \
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+ python ${base_directory}/plot_skull_strip.py \
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+ --mask-file "${mask_file}" \
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+ --background-file "${synthseg_directory}/t1w.nii.gz" \
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+ --output-file "${report_file}"
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+
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+subject_id=$(basename "$(find "${derivatives_directory}"/fmriprep/* -maxdepth 0 -print -quit)")
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+fmriprep_directory=$(find "${derivatives_directory}"/fmriprep/"${subject_id}"/ses-* -maxdepth 0 -print -quit)
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+
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+transform_suffix="_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5"
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+transform_file=$(find "${derivatives_directory}" -name "*${transform_suffix}" -print -quit)
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+jacobian_file=$(dirname "${transform_file}")/$(basename "${transform_file}" ${transform_suffix})_jacobian.nii.gz
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+singularity exec \
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+ --cleanenv \
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+ --bind /tmp \
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+ ${halfpipe_container} \
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+ python ${base_directory}/calculate_jacobian.py \
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+ --transform-file "${transform_file}" \
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+ --output-file "${jacobian_file}"
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+
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+mapfile -t anat_files < <(find "${fmriprep_directory}"/anat \( -name "*.nii.gz" -o -name "*.json" \) -not -name "*_desc-preproc_T1w.nii.gz" -print)
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+
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+tar_file="${base_directory}/halfpipe/${subject_id}.tar"
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+tar --verbose \
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+ --create \
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+ --dereference \
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+ --file="${tar_file}" \
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+ "${halfpipe_directory}"/reports/"${subject_id}" \
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+ "${derivatives_directory}"/halfpipe/"${subject_id}" \
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+ "${fmriprep_directory}"/func \
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+ "${anat_files[@]}"
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+zstd --ultra --threads=0 -22 "${tar_file}"
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+
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+rm "${tar_file}"
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+rm -rf "${dataset_directory}" "${bids_directory}" "${halfpipe_directory}"
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