setup_input_image.sh

#!/bin/bash

# Uncomment if running from the command line
#module load fsl
#module load ants
#module load python3/3.8.3_anaconda2020.07_mamba 

FSLDIR=/panfs/roc/msisoft/fsl/6.0.2

input=$1
WD=$2
output=$3

mkdir -p ${WD}

# Create naming shceme for intermediate files. Assumes all images end in .nii.gz

std=$WD/`basename $input | sed 's|.nii.gz|_std.nii.gz|'`
acpc=$WD/`basename $input | sed 's|.nii.gz|_acpc.nii.gz|'`
omat=`echo $acpc | sed 's|.nii.gz|.mat|'`
denoised=`echo $acpc | sed 's|.nii.gz|Denoise.nii.gz|'`
dc=`echo $denoised | sed 's|.nii.gz|N4dc.nii.gz|'`

# Run initial modality independent stages of PreFreeSurfer

fslreorient2std ${input} ${std}

if [[ $input == *T1w*  ]]; then
    /home/faird/shared/projects/3D_MRI_GAN/tio_unet/dcan-infant-pipeline/PreFreeSurfer/scripts/ACPCAlignment_with_crop.sh --workindir=${WD} --in=${std} --ref=/home/faird/shared/projects/3D_MRI_GAN/tio_unet/dcan-infant-pipeline/global/templates/INFANT_MNI_T1_1mm.nii.gz --out=$acpc --omat=$omat --brainsize=120
else
    /home/faird/shared/projects/3D_MRI_GAN/tio_unet/dcan-infant-pipeline/PreFreeSurfer/scripts/ACPCAlignment_with_crop.sh --workindir=${WD} --in=${std} --ref=/home/faird/shared/projects/3D_MRI_GAN/tio_unet/dcan-infant-pipeline/global/templates/INFANT_MNI_T2_1mm.nii.gz --out=$acpc --omat=$omat --brainsize=120
fi

DenoiseImage -d 3 -n Rician --input-image ${acpc} --output ${denoised}

# Removed Bias Field Correction
#N4BiasFieldCorrection -d 3 --input-image ${denoised} --shrink-factor 2 --output [${dc},${WD}/N4BiasField_T1.nii.gz]

mkdir -p `dirname ${output}`

#cp ${dc} ${output_dir}/${subject}_${session}_T1w.nii.gz
cp ${denoised} ${output}