find_3d_thresh

#! /bin/bash
# ------------------------------------------------------------------------------
# Script name:  find_3d_thresh.sh
#
# Description:  Find the appropriate thresholding to reconstruct faces from different input modalities.
#
# Author:       Caroline Nettekoven, 2020
#
# ------------------------------------------------------------------------------
# ------------------------------------------------------------------------------
input_dir=/Users/CN/Documents/Projects/BOLD_study_local/deidentification/example_subject/sub-650BT/
output_dir=${input_dir}/defaced
tool_dir=/Users/CN/Documents/Projects/BOLD_study_local/bin/
py_dir=/Users/CN/Documents/Projects/Joystick_Cereb_MRS/bin/mrsi_code/env/bin
# ------------------------------------------------------------------------------
images_to_deface=" anat/sub-650BT_T1w_nrm.nii.gz \
anat/sub-650BT_T1w_raw.nii.gz \
dwi/sub-650BT_acq-AP_dwi.nii.gz \
dwi/sub-650BT_acq-AP_sbref.nii.gz \
dwi/sub-650BT_acq-PA_dwi.nii.gz \
dwi/sub-650BT_acq-PA_sbref.nii.gz \
func/sub-650BT_task-nwr_bold.nii.gz \
func/sub-650BT_task-nwr_sbref.nii.gz \
func/sub-650BT_task-rest_bold.nii.gz \
func/sub-650BT_task-rest_sbref.nii.gz \
func/sub-650BT_task-verbgen_bold.nii.gz \
func/sub-650BT_task-verbgen_sbref.nii.gz "
# ------------------------------------------------------------------------------

for image in ${images_to_deface}; do
    echo "Generating qc image for ${image}..."

    img=${input_dir}/${image}
    img_stem=${image#*BT_}
    img_stem=${img_stem%.nii*}


    # Copy and face reconstruct original image:
    dim=`echo "\`${FSLDIR}/bin/fslval ${img} dim3\` /2" |bc ` ;
    ${FSLDIR}/bin/fslroi ${img} ${output_dir}/${img_stem}_orig 0 -1 0 -1 ${dim} 1;

    # Set threshold dependent on modality
    # if [[ ${image:0:3} == "ana"]]; then
    #     thr=35
    # elif [[ ${image:0:3} == "fun"]]; then
    #     thr=55
    # elif [[ ${image:0:3} == "dwi"]]; then
    #     thr=55
    # elif [[ ${image:0:3} == "mpm"]]; then
    #     thr=55
    # fi

    for thr in 30 35 40 45 50 55 60 65 70 75 80; do
    sh ${tool_dir}/fsl_gen_3D_crn_thr \
                ${img} \
                ${output_dir}/thresholding/${img_stem}_orig_thr${thr} \
                ${thr}
    done

done

# thresholds to get face reconstruction:
# For functional data: 55
# For anat data: 35