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ENH: Add SCILPY prepare shell data singularity alternative script
Add `SCILPY` prepare shell data singularity alternative script.
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‎scripts/scilpy_prepare_shell_data_singularity.sh

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#!/bin/bash
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usage()
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{
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echo "usage: $(basename $0) [-h] [in_qsiprep_dirname] [out_dirname] [work_dirname] [in_nifti_fname] [in_bval_fname] [in_bvec_fname] [scilus_singularity_fname] [szbd_singularity_fname] [participant]"
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echo
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echo "Prepare preprocessed dMRI shell data for UKF tractography using SCILPY."
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echo
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echo "positional arguments:"
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echo " in_qsiprep_dirname Input data dirname"
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echo " out_dirname Output dirname"
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echo " work_dirname Singularity work dirname"
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echo " in_nifti_fname Input NIfTI filename (*.nii.gz)"
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echo " in_bval_fname Input bval filename (*.bval)"
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echo " in_bvec_fname Input bvec filename (*.bvec)"
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echo " scilus_singularity_fname Scilus singularity filename (*.sif)"
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echo " szbd_singularity_fname SZBD singularity filename (*.sif)"
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echo " participant Participant ID"
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echo
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echo "optional arguments:"
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echo " -h, --help show this help message and exit"
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1>&2; exit 1;
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}
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# Parse input arguments
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args=""
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while (( "$#" )); do
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case "$1" in
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"-h"|"--help")
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usage
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;;
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-*|--*=) # unsupported flags
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echo "Error: Unsupported flag $1" >&2
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usage
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;;
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*) # preserve positional arguments
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args="$args $1"
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shift
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;;
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esac
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done
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# Set positional arguments in their proper place
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eval set -- "$args"
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if test "${args[@]}" = "" || [ "$#" -lt 9 ]; then
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echo "Missing arguments."
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usage
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fi
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in_qsiprep_dirname=$1
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out_root_dirname=$2
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work_dirname=$3
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in_nifti_fname=$4
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in_bval_fname=$5
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in_bvec_fname=$6
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scilus_singularity_fname=$7
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szbd_singularity_fname=$8
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participant=$9
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dash="-"
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ext_sep="."
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bval_ext="bval"
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bvec_ext="bvec"
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nii_gz_ext="nii.gz"
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underscore="_"
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fourd_label="4d"
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bval_label="b"
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b0_mean_label="b0_mean"
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function compose_filename_from_basename() {
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local in_fname="$1"
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local out_dirname="$2"
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local label="$3"
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local ext="$4"
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# Get the basename without external command by stripping out longest leading
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# match of anything followed by /
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local base_fname=${in_fname##*/}
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# Strip all extensions by stripping out longest trailing match of dot
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# followed by anything
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local root_fname=${base_fname%%.*}
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echo ${out_dirname}/${root_fname}${underscore}${label}${ext_sep}${ext}
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}
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# Create the output dirname
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out_participant_dirname=${out_root_dirname}/${participant}
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mkdir ${out_participant_dirname}
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out_dirname=${out_participant_dirname}/dwi
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mkdir ${out_dirname}
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# Extract mean b0
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# https://scilpy.readthedocs.io/en/stable/scripts/scil_dwi_extract_b0.html
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b0_thr=20
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out_b0_mean_fname=$(compose_filename_from_basename ${in_nifti_fname} ${out_dirname} ${b0_mean_label} ${nii_gz_ext})
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singularity exec \
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--bind ${in_qsiprep_dirname} \
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--bind ${out_dirname} \
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--bind ${work_dirname} \
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--workdir ${work_dirname} \
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${scilus_singularity_fname} \
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scil_dwi_extract_b0.py \
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${in_nifti_fname} \
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${in_bval_fname} \
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${in_bvec_fname} \
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${out_b0_mean_fname} \
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--b0_thr ${b0_thr} \
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--mean
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echo "Mean b0 written to:"
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echo ${out_b0_mean_fname}
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# Expand dimension to mean b0 data
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out_b0_mean_4d_nifti_fname=$(compose_filename_from_basename ${out_b0_mean_fname} ${out_dirname} ${fourd_label} ${nii_gz_ext})
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singularity exec \
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--bind ${out_dirname} \
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--bind ${work_dirname} \
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--workdir ${work_dirname} \
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${szbd_singularity_fname} \
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expand_dims_nifti.py \
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${out_b0_mean_fname} \
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${out_b0_mean_4d_nifti_fname}
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echo "Mean b0 as 4D volume written to:"
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echo ${out_b0_mean_4d_nifti_fname}
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# Create empty b0 bval and bvec
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out_b0_mean_4d_bval_fname=$(compose_filename_from_basename ${out_b0_mean_fname} ${out_dirname} ${fourd_label} ${bval_ext})
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out_b0_mean_4d_bvec_fname=$(compose_filename_from_basename ${out_b0_mean_fname} ${out_dirname} ${fourd_label} ${bvec_ext})
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singularity exec \
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--bind ${out_dirname} \
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--bind ${work_dirname} \
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--workdir ${work_dirname} \
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${szbd_singularity_fname} \
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create_mean_b0_bval_bvec_files.py \
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${out_b0_mean_4d_bval_fname} \
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${out_b0_mean_4d_bvec_fname}
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echo "Mean b0 bval and bvec files written to:"
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echo ${out_b0_mean_4d_bval_fname}
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echo ${out_b0_mean_4d_bvec_fname}
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# Extract b-value
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# https://scilpy.readthedocs.io/en/stable/scripts/scil_dwi_extract_shell.html
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bval=3000
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bval_tol=100
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bval_shell_label=${bval_label}${bval}
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out_bval_shell_nifti_fname=$(compose_filename_from_basename ${in_nifti_fname} ${out_dirname} ${bval_shell_label} ${nii_gz_ext})
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out_bval_shell_bval_fname=$(compose_filename_from_basename ${in_nifti_fname} ${out_dirname} ${bval_shell_label} ${bval_ext})
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out_bval_shell_bvec_fname=$(compose_filename_from_basename ${in_nifti_fname} ${out_dirname} ${bval_shell_label} ${bvec_ext})
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singularity exec \
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--bind ${in_qsiprep_dirname} \
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--bind ${out_dirname} \
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--bind ${work_dirname} \
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--workdir ${work_dirname} \
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${scilus_singularity_fname} \
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scil_dwi_extract_shell.py \
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${in_nifti_fname} \
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${in_bval_fname} \
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${in_bvec_fname} \
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${bval} \
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${out_bval_shell_nifti_fname} \
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${out_bval_shell_bval_fname} \
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${out_bval_shell_bvec_fname} \
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--tolerance ${bval_tol}
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echo "b${bval} files written to:"
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echo ${out_bval_shell_nifti_fname}
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echo ${out_bval_shell_bval_fname}
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echo ${out_bval_shell_bvec_fname}
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# Concatenate mean b0 and b-value data
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# https://scilpy.readthedocs.io/en/stable/scripts/scil_dwi_concatenate.html
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b0_mean_bval_shell_label=${b0_mean_label}${dash}${bval_label}${bval}
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out_b0_mean_bval_shell_nifti_fname=$(compose_filename_from_basename ${in_nifti_fname} ${out_dirname} ${b0_mean_bval_shell_label} ${nii_gz_ext})
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out_b0_mean_bval_shell_bval_fname=$(compose_filename_from_basename ${in_nifti_fname} ${out_dirname} ${b0_mean_bval_shell_label} ${bval_ext})
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out_b0_mean_bval_shell_bvec_fname=$(compose_filename_from_basename ${in_nifti_fname} ${out_dirname} ${b0_mean_bval_shell_label} ${bvec_ext})
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singularity exec \
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--bind ${in_qsiprep_dirname} \
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--bind ${out_dirname} \
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--bind ${work_dirname} \
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--workdir ${work_dirname} \
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${scilus_singularity_fname} \
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scil_dwi_concatenate.py \
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${out_b0_mean_bval_shell_nifti_fname} \
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${out_b0_mean_bval_shell_bval_fname} \
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${out_b0_mean_bval_shell_bvec_fname} \
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--in_dwis \
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${out_b0_mean_4d_nifti_fname} \
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${out_bval_shell_nifti_fname} \
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--in_bvals \
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${out_b0_mean_4d_bval_fname} \
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${out_bval_shell_bval_fname} \
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--in_bvecs \
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${out_b0_mean_4d_bvec_fname} \
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${out_bval_shell_bvec_fname}
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echo "Concatenated b0 and b${bval} files written to:"
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echo ${out_b0_mean_bval_shell_nifti_fname}
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echo ${out_b0_mean_bval_shell_bval_fname}
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echo ${out_b0_mean_bval_shell_bvec_fname}

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