MNI tractography

dti_mni_tractography.sh

for i in $@
do
    echo ${i}
    MNIdir=${i}/DTI_MNI
    if [ ! -d ${MNIdir} ]
    then
        mkdir ${MNIdir}
    fi  

    # MNI registration
    for img in ${i}/DTI/data_eddy.nii.gz ${i}/DTI/nodif_brain_mask.nii.gz
    do
        echo registering ${img}
        imgBase=`basename ${img}`
        imgName=${imgBase%.nii.gz*}

        if [ ! -e ${MNIdir}/${imgBase} ]
        then
            flirt -in ${img} \
                -ref ${FSLDIR}/data/standard/MNI152_T1_2mm.nii.gz \
                -applyxfm -init ${i}/registration/nodifToMNI.mat \
                -out ${MNIdir}/${imgBase}
        fi
    done

    # DTIfit
    if [ ! -e ${MNIdir}/DTI_FA.nii.gz ]
    then
        dtifit -k ${MNIdir}/data_eddy.nii.gz \
            -o ${MNIdir}/DTI \
            -m ${MNIdir}/nodif_brain_mask.nii.gz \
            -r ${i}/DTI/bvecs \
            -b ${i}/DTI/bvals
    fi

    cp ${MNIdir}/data_eddy.nii.gz ${MNIdir}/data.nii.gz

    # Bedpostx
    ${bedpostDir}=${MNIdir}.bedpostX

    if [ -d ${bedpostDir} ]
    then
        bedpostx ${MNIdir}
    fi

    # Tractography
    ${mniThalROI}=/Volume/CCNC_W1_2T/2017_CHR_thalamus_microstructure_kcho/allData/scripts/lh_thalamus_HOSC_60.nii.gz
    ${tractDir}=${i}/tractography


    if [ ! -e ${tractDir}/fdt_paths.nii.gz ]
    then
        rm -rf ${tractDir}
        mkdir -p ${tractDir}
        probtrackx2 \
            -x ${mniThalROI} \
            -l \
            --onewaycondition \
            --omatrix2 \
            --target2=${bedpostDir}/nodif_brain_mask.nii.gz \
            -c 0.2 \
            -S 2000 \
            --steplength=0.5 \
            -P 5000 \
            --fibthresh=0.01 \
            --distthresh=0.0 \
            --sampvox=0.0 \
            --forcedir \
            --opd \
            -s ${bedpostDir}/merged \
            -m ${bedpostDir}/nodif_brain_mask \
            --dir=${tractDir}
    fi
 
    if [ -e ${tractDir}/fdt_matrix2_reconstructed.nii.gz ]
    then
        postProcessing=/Volume/CCNC_W1_2T/2017_CHR_thalamus_microstructure_kcho/allData/scripts/tracktography/postprocessing/probtrackx_postprocessing.py
 
        python  ${postProcessing} \
            ${tractDir} \
            ${bedpostDir}/nodif_brain_mask.nii.gz
    fi
 
done