halfpipe_containers/code/halfpipe.sh

#!/bin/bash
#$ -N halfpipe
#$ -q compute7.q
#$ -j y
#$ -o halfpipe.log.txt
#$ -cwd
#$ -pe smp 2 -binding linear
#$ -l h_rt=48:0:0
#$ -l virtual_free=20480M

#$ -t 101-10000

set -e
set -x

base_directory=/ifs/loni/faculty/njahansh/collaborators/lea/ukbiobank
clinical_directory=${base_directory}/clinical_data

dataset_directory=$(mktemp -d)
bids_directory=$(mktemp -d)
synthseg_directory=$(mktemp -d)
halfpipe_directory=$(mktemp -d)

synthseg_container=${base_directory}/synthseg.sif
halfpipe_container=${base_directory}/halfpipe-latest-240307.sif

read -r -a files < <(sed -n "${SGE_TASK_ID}p" ${base_directory}/tasks.txt)

for file in "${files[@]}"; do
    ln -s "${file}" "${dataset_directory}"
done

mamba run --name clinica \
    clinica convert ukb-to-bids \
    "${dataset_directory}" \
    "${clinical_directory}" \
    "${bids_directory}"

t1w_file=$(find "${bids_directory}" -name "*_T1w.nii.gz" -print -quit)
mv -v "${t1w_file}" "${synthseg_directory}/t1w.nii.gz"

singularity run \
    --bind "${synthseg_directory}" \
    ${synthseg_container} \
    --i "${synthseg_directory}/t1w.nii.gz" \
    --o "${synthseg_directory}/synthseg.nii.gz" \
    --robust \
    --cpu --threads 1

singularity exec \
    --bind "${synthseg_directory}" \
    ${halfpipe_container} \
    antsApplyTransforms \
    --dimensionality 3 \
    --input "${synthseg_directory}/synthseg.nii.gz" \
    --reference-image "${synthseg_directory}/t1w.nii.gz" \
    --output "${synthseg_directory}/synthseg_in_t1w_space.nii.gz" \
    --interpolation MultiLabel \
    --verbose

singularity exec \
    --bind "${base_directory}" \
    --bind "${synthseg_directory}" \
    ${halfpipe_container} \
    ${base_directory}/apply_mask.py \
    "${synthseg_directory}/t1w.nii.gz" \
    "${synthseg_directory}/synthseg_in_t1w_space.nii.gz" \
    "${t1w_file}"

cat <<EOF >"${halfpipe_directory}/spec.json"
{
    "halfpipe_version": "1.2.2.post1.dev535+gc31d205",
    "schema_version": "3.0",
    "timestamp": "2023-08-08_16-01",
    "global_settings": {
        "dummy_scans": 0,
        "slice_timing": true,
        "use_bbr": null,
        "skull_strip_algorithm": "none",
        "run_mriqc": false,
        "run_fmriprep": true,
        "run_halfpipe": true,
        "fd_thres": 0.5,
        "anat_only": false,
        "write_graph": false,
        "hires": false,
        "run_reconall": false,
        "t2s_coreg": false,
        "medial_surface_nan": false,
        "bold2t1w_dof": 9,
        "fmap_bspline": true,
        "force_syn": false,
        "longitudinal": false,
        "regressors_all_comps": false,
        "regressors_dvars_th": 1.5,
        "regressors_fd_th": 0.5,
        "skull_strip_fixed_seed": false,
        "skull_strip_template": "OASIS30ANTs",
        "aroma_err_on_warn": false,
        "aroma_melodic_dim": -200,
        "sloppy": false
    },
    "files": [
        {
            "metadata": {},
            "datatype": "bids",
            "path": "${bids_directory}"
        },        
        {
            "suffix": "events",
            "path": "${bids_directory}/task-{task}_events.tsv",
            "extension": ".tsv",
            "datatype": "func"
        }
    ],
    "settings": [
        {
            "ica_aroma": true,
            "smoothing": {
                "fwhm": 6.0
            },
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "bandpass_filter": {
                "hp_width": 125.0,
                "lp_width": null,
                "type": "gaussian"
            },
            "name": "icaAromaSetting",
            "filters": [
                {
                    "type": "tag",
                    "action": "include",
                    "values": [
                        "facesshapesemotion"
                    ],
                    "entity": "task"
                }
            ],
            "output_image": false
        },
        {
            "ica_aroma": false,
            "smoothing": {
                "fwhm": 6.0
            },
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "bandpass_filter": {
                "hp_width": 125.0,
                "lp_width": null,
                "type": "gaussian"
            },
            "confounds_removal": [
                "(trans|rot)_[xyz]"
            ],
            "name": "motionParametersSetting",
            "filters": [
                {
                    "type": "tag",
                    "action": "include",
                    "values": [
                        "facesshapesemotion"
                    ],
                    "entity": "task"
                }
            ],
            "output_image": false
        },
        {
            "ica_aroma": false,
            "smoothing": {
                "fwhm": 6.0
            },
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "bandpass_filter": {
                "hp_width": 125.0,
                "lp_width": null,
                "type": "gaussian"
            },
            "name": "noConfoundsSetting",
            "filters": [
                {
                    "type": "tag",
                    "action": "include",
                    "values": [
                        "facesshapesemotion"
                    ],
                    "entity": "task"
                }
            ],
            "output_image": false
        }
    ],
    "features": [
        {
            "name": "icaAroma",
            "setting": "icaAromaSetting",
            "contrasts": [
                {
                    "type": "t",
                    "name": "faceNegVsControl",
                    "values": {
                        "Face": 1.0,
                        "Shape": -1.0
                    }
                }
            ],
            "hrf": "dgamma",
            "conditions": [
                "Face",
                "Shape"
            ],
            "type": "task_based",
            "high_pass_filter_cutoff": 125.0
        },
        {
            "name": "motionParameters",
            "setting": "motionParametersSetting",
            "contrasts": [
                {
                    "type": "t",
                    "name": "faceNegVsControl",
                    "values": {
                        "Face": 1.0,
                        "Shape": -1.0
                    }
                }
            ],
            "hrf": "dgamma",
            "conditions": [
                "Face",
                "Shape"
            ],
            "type": "task_based",
            "high_pass_filter_cutoff": 125.0
        },
        {
            "name": "noConfounds",
            "setting": "noConfoundsSetting",
            "contrasts": [
                {
                    "type": "t",
                    "name": "faceNegVsControl",
                    "values": {
                        "Face": 1.0,
                        "Shape": -1.0
                    }
                }
            ],
            "hrf": "dgamma",
            "conditions": [
                "Face",
                "Shape"
            ],
            "type": "task_based",
            "high_pass_filter_cutoff": 125.0
        }
    ],
    "models": []
}
EOF

singularity run \
    --contain \
    --cleanenv \
    --bind /tmp \
    ${halfpipe_container} \
    --workdir "${halfpipe_directory}" \
    --skip-spec-ui \
    --nipype-n-procs "$(nproc)" \
    --keep none

derivatives_directory=${halfpipe_directory}/derivatives
mask_file=$(find "${derivatives_directory}" -name "*_desc-brain_mask.nii.gz" \( -not -name "*space*" \) -print -quit)
report_file=$(find "${halfpipe_directory}/reports" -name "*_skull_strip_report*svg" -print -quit)

singularity exec \
    --bind /tmp \
    ${halfpipe_container} \
    python ${base_directory}/plot_skull_strip.py \
    --mask-file "${mask_file}" \
    --background-file "${synthseg_directory}/t1w.nii.gz" \
    --output-file "${report_file}"

subject_id=$(basename "$(find "${derivatives_directory}"/fmriprep/* -maxdepth 0 -print -quit)")
fmriprep_directory=$(find "${derivatives_directory}"/fmriprep/"${subject_id}"/ses-* -maxdepth 0 -print -quit)

transform_suffix="_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5"
transform_file=$(find "${derivatives_directory}" -name "*${transform_suffix}" -print -quit)
jacobian_file=$(dirname "${transform_file}")/$(basename "${transform_file}" ${transform_suffix})_jacobian.nii.gz
singularity exec \
    --cleanenv \
    --bind /tmp \
    ${halfpipe_container} \
    python ${base_directory}/calculate_jacobian.py \
    --transform-file "${transform_file}" \
    --output-file "${jacobian_file}"

mapfile -t anat_files < <(find "${fmriprep_directory}"/anat \( -name "*.nii.gz" -o -name "*.json" \) -not -name "*_desc-preproc_T1w.nii.gz" -print)

tar_file="${base_directory}/halfpipe/${subject_id}.tar"
tar --verbose \
    --create \
    --dereference \
    --file="${tar_file}" \
    "${halfpipe_directory}"/reports/"${subject_id}" \
    "${derivatives_directory}"/halfpipe/"${subject_id}" \
    "${fmriprep_directory}"/func \
    "${anat_files[@]}"
zstd --ultra --threads=0 -22 "${tar_file}"

rm "${tar_file}"
rm -rf "${dataset_directory}" "${bids_directory}" "${halfpipe_directory}"