A Reproducible Diffusion MRI Processing Pipeline for Microstructure and Glymphatic Analysis Using Neurodesk Containers

await lmod.load(bidscoin/4.6.2)

#Scan DICOMs and generate the initial mapping
!bidsmapper $SOURCE_DICOM_DIR $BIDS_DIR

import os
import shutil

# Define the source template bidsmap and the target location
TEMPLATE_BIDS_MAP = /root/.bidscoin/4.6.2/templates/bidsmap_dccn.yaml
BIDSMAP_DIR = os.path.join(BIDS_DIR, code/bidscoin)
BIDSMAP_FILE = os.path.join(BIDSMAP_DIR, bidsmap.yaml)

# Create the target directory if it doesnt exist
os.makedirs(BIDSMAP_DIR, exist_ok=True)

# Copy the template bidsmap to the target location
shutil.copy(TEMPLATE_BIDS_MAP, BIDSMAP_FILE)

print(fCopied template bidsmap to: {BIDSMAP_FILE})

# Execute the conversion based on the mapping
!bidscoiner $SOURCE_DICOM_DIR $BIDS_DIR

await lmod.load(mriqc/24.0.2)

!mriqc $BIDS_DIR $DERIVATIVES/mriqc participant --participant-label <SUBJECT_ID> -w /content/workdir --mem_gb [MEMORY_GIGABYTE] --nprocs [N_CPUS] --no-sub

await lmod.load(fmriprep/25.1.3)

# Ensure FreeSurfer license is present
!export FS_LICENSE=[PATH_TO_YOUR_FREESURFER_LICENSE]

!fmriprep $BIDS_DIR $DERIVATIVES/fmriprep participant --participant-label <SUBJECT_ID> --w /content/work_dir --mem [MEMORY_MEGABYTE] --nprocs [N_CPUS] --anat-only --fs-license-file $FS_LICENSE --fs-no-reconall

!curl -Ls https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/getfsl.sh | sh -s -- ~/fsl/ --extra truenet

!update_fsl_release --extra truenet

%%bash
RAW_DIR=$PROJECT_DIR/rawdata
TRUENET_DIR=$DERIVATIVES/truenet

for SUB in ${RAW_DIR}/sub-*; do
    SUB_ID=$(basename ${SUB})
    
    echo ------------------------------------------------
    echo Preparing TrUE-Net data for: ${SUB_ID}
    echo ------------------------------------------------

    # Create a subject-specific output directory in truenet derivatives
    mkdir -p ${TRUENET_DERIV}/${SUB_ID}/prepared_data

    prepare_truenet_data --FLAIR=${SUB_PATH}/anat/${SUB_ID}_*FLAIR.nii.gz --T1=${SUB_PATH}/anat/${SUB_ID}_*T1w.nii.gz --outname=${TRUENET_DERIV}/${SUB_ID}/prepared/${SUB_ID}

done

%%bash
for SUB in ${TRUENET_DIR}/sub-*; do
    SUB_ID=$(basename ${SUB})

    echo Segmenting WMH for: ${SUB_ID}

    mkdir -p ${TRUENET_DIR}/${SUB_ID}/truenet_results

    truenet evaluate -m mwsc -i ${TRUENET_DIR}/${SUB_ID}/prepared_data -o ${TRUENET_DIR}/${SUB_ID}/truenet_results
done

ml qsiprep/1.0.1
!qsiprep $BIDS_DIR $DERIVATIVES/qsiprep participant --participant-label <SUBJECT_ID> -w $QSIPREP_WORK_DIR --dwi-only --fs-license-file $FS_LICENSE --output-resolution [VOXEL_SIZE_IN_MM] --nprocs [N_CPUS] --mem [MEMORY_MEGABYTE]

await lmod.load(qsirecon/1.1.0)

!qsirecon $DERIVATIVES/qsiprep $DERIVATIVES/qsirecon participant --participant-label <SUBJECT_ID> --recon-spec [RECON_SPEC] -w $QSIRECON_WORK_DIR --fs-license-file $FS_LICENSE --fs-subjects-dir $FS_DIR --atlases 4S --output-resolution [VOXEL_SIZE_IN_MM] --nprocs [N_CPUS] --mem [MEMORY_MEGABYTE]

%cd $DERIVATIVES/dti_alps

!git clone https://github.com/Winniework/Automated-DTI-ALPS-pipeline.git

# Loop through subjects to organize data
for SUB_DIR in ${BIDS_DIR}/sub-*; do
    SUB=$(basename ${SUB_DIR})
    TARGET_DIR=${DERIVATIVES}/dti_alps/${SUB}
    
    echo Preparing ${SUB}...
    mkdir -p ${TARGET_DIR}

    # Copy the template from the cloned repo into each subject folder
    cp ${DERIVATIVES}/dti_alps/Automated-DTI-ALPS-pipeline/ICBM_FA.nii.gz ${TARGET_DIR}/

    # Copy raw BIDS files (using wildcards to stay generic)
    cp ${SUB_DIR}/dwi/${SUB}_*dwi.nii.gz ${TARGET_DIR}/dti.nii.gz
    cp ${SUB_DIR}/dwi/${SUB}_*dwi.bval ${TARGET_DIR}/dti.bval
    cp ${SUB_DIR}/dwi/${SUB}_*dwi.bvec ${TARGET_DIR}/dti.bvec
done

# Load required software modules
await lmod.load(mrtrix3/3.0.4)
await lmod.load(fsl/6.0.7.18)
await lmod.load(ants/2.6.0)
await lmod.load(afni/25.2.03)

%cd $DERIVATIVES/dti_alps
for SUB in sub-*; do
    if [ -d $SUB ]; then
        echo Processing $SUB...
        cd $SUB
       
        bash ../Automated-DTI-ALPS-pipeline/1_DTI_preprocessing.sh
        cd ..
    fi
done

# Ensure you are in the dti_alps directory where all sub- folders exist
%cd $DERIVATIVES/dti_alps

# Execute the automated calculation
!python Automated-DTI-ALPS-pipeline/2_Automated_DTI-ALPS.py