lnifmri_prep00_organize

#!/bin/bash
#
# LNiF MRI Lab Pipeline for preprocessing of
# structural and functional MRI dataset
# stefano.tambalo@unitn.it - 20200310
#
# Organize raw data in a convenient directory structure.
# We recommend dcm2niix for DICOM to NIFTI conversion with
# the following flags:
#               
# dcm2niix -f %f_%p_%i_%t_%s -b y -ba n -z y <FOLDER NAME>
#
########################################################################
export LC_ALL=C

shopt -s extglob
 
Usage() {
    printf "\n***************************************************\n"
    printf "LNiF MRI Lab Preprocessing Pipeline\n"
    printf "CIMeC - Center for Mind/Brain Science\n\n"
    printf "\tRequires:\n\t\t--\n"
    printf "\tUsage:\n\t\tlnifmri_prep00_organize -o outdir\n"
    printf "\tArgs:\n"
    printf "\t\t-o:\tspecify name of main output directory;\n\n"
    printf "\te.g.:\tlnif_preproc_00_organize -o my_project_root"
    printf "\n\n(c) stefano.tambalo@unitn.it, 2020.\n"
    printf "***************************************************\n\n"
    exit 1
}

Start() {
    stamp=`date +%Y%m%d_%H%M%S`
    printf "\n***************************************************\n"
    printf "LNiF MRI Lab Preprocessing Pipeline\n"
    printf "CIMeC - Center for Mind/Brain Science\n\n"
    printf "Create directory structure\n"    
    printf "\n\tOutput Directory: $OUTDIR\n\n"
}

NextStep() {
    printf "\n****************************************************\n"
    printf "LNiF MRI Lab Preprocessing Pipeline\n"
    printf "CIMeC - Center for Mind/Brain Science\n\n"
    printf "Complete. Exec. Time: ${exectime}\nNow cd to $OUTDIR\nand run lnifmri_prep01_anat\n"
    printf "\n++++++++++++++++    [ HINT ]    ++++++++++++++++++++\n"
    printf "To save time, run:\n\tcd <my_project_root>\n\tlnifmri_prep01_anat &\n\tlnifmri_prep02_preproc"
    printf "\n\n****************************************************\n\n"
    exit 1
}

[ "$1" = "" ] && Usage

# Set default directories
SUBDIR=""
SUBPATH=""
DIRNAME=""
OUTDIR=""
ANATDIR="anat"
FUNCDIR="func"
BOLDDIR="bold"
RESTDIR="rest"
DWIDIR="dwi"
SDCDIR="sdc"
TOFDIR="tof"
ASLDIR="asl"
SWIDIR="swi"
MISCDIR="misc"
QCDIR="qc"
subcount=0

DATAPATH=`pwd`
#echo $DATAPATH

#Get name of output directory
while getopts o: option
    do
        case "${option}" in
            o) DIRNAME=${OPTARG};;
        esac
    done

#Set fullpath of DIRNAME
OUTDIR=$DATAPATH/$DIRNAME
LOGDIR=$DATAPATH/$DIRNAME/logs
exectime=0
SECONDS=0
stamp=`date +%Y%m%d_%H%M%S`

Start

#DICOM conversion
for DCMDIR in `cat lnifmri_prep_dcmlist.txt` ; do    
    printf "${DCMDIR}: DICOM to NIFTI conversion\n"
    #check if current directory is an output dir from lnifmri_prep;
    #if not, run the DCM to NII conversion of image files
    if [ -f "${DCMDIR}/lnifmri_prep_output.txt" ]; then
        
        printf "\t${DCMDIR}: not a raw DICOM folder.\n"

    else

    	dcm2niix -f %f_%p_%t_%s_%d -b y -ba n -z y ${DCMDIR}
        sleep 1
		printf "LNiF MRI Lab Preprocessing Pipeline\nDo not remove this file!\nCreated: ${stamp}" >> ${DCMDIR}/lnifmri_prep_output.txt
        mv ${DCMDIR} ${DCMDIR}.sub
        printf "%s\n" "${DCMDIR}.sub" >> lnifmri_prep_sublist.txt
    fi
done
printf "\n\nConversion complete. Setting up the environment \n\n\n"

#Prepare the output directory tree
#for SUBRAW in *.sub ; do
#for SUBRAW in `cat lnifmri_prep_sublist.txt` ; do
for SUBPATH in `cat lnifmri_prep_sublist.txt` ; do    
    #SUBPATH=$DATAPATH/$SUBRAW
    #echo $SUBPATH
    printf -v SUBDIR -- 'sub-%02d' "$(( ++subcount ))"
    #echo $SUBDIR

    mkdir   -p -m 777 \
            $OUTDIR/$SUBDIR \
            $OUTDIR/$SUBDIR/$ANATDIR \
            $OUTDIR/$SUBDIR/$FUNCDIR \
            $OUTDIR/$SUBDIR/$DWIDIR \
            $OUTDIR/$SUBDIR/$SDCDIR \
            $OUTDIR/$SUBDIR/$TOFDIR \
            $OUTDIR/$SUBDIR/$ASLDIR \
            $OUTDIR/$SUBDIR/$SWIDIR \
            $OUTDIR/$SUBDIR/$MISCDIR;

    #copy dataset into the corresponding directory
    for f in $SUBPATH/*.{nii,nii.gz,json,bval,bvec} ; do
    # for f in $SUBPATH/*.* ; do
        #extract basename
        u=`basename $f`
        # fix invalid characters
        d=`echo ${u} | sed -e 's/[^A-Za-z0-9._-]/_/g'`
        #printf "$f\n"
        #printf "$d\n\n"
        case "${d}" in
            *MEmprage*_e[1-9]*)
                printf "Copy echo data\t${d}\n"
                cp $f $OUTDIR/$SUBDIR/$MISCDIR/$d
                ;;
            *bold*)
                printf "Copy func data\t${d}\n"
                cp $f $OUTDIR/$SUBDIR/$FUNCDIR/$d
                ;;
            *fMRI*) #GE specific
                printf "Copy func data\t${d}\n"
                cp $f $OUTDIR/$SUBDIR/$FUNCDIR/$d
                ;;
            *t1*)
                printf "Copy anat data\t${d}\n"
                cp $f $OUTDIR/$SUBDIR/$ANATDIR/$d
                ;;
            *mask*)
                printf "Copy mask data\t${d}\n"
                cp $f $OUTDIR/$SUBDIR/$ANATDIR/$d
                ;;
            *T1*) #GE specific 2022-06-07
                printf "Copy anat data\t${d}\n"
                cp $f $OUTDIR/$SUBDIR/$ANATDIR/$d
                ;;                
            *t2*)
                printf "Copy T2w data\t${d}\n"
                cp $f $OUTDIR/$SUBDIR/$MISCDIR/$d
                ;;
            *T2*)
                printf "Copy T2w data\t${d}\n"
                cp $f $OUTDIR/$SUBDIR/$MISCDIR/$d
                ;;
            *MSHELL*)
                printf "Copy diff data\t${d}\n"
                cp $f $OUTDIR/$SUBDIR/$DWIDIR/$d
                ;;
            *mshell*)
                printf "Copy diff data\t${d}\n"
                cp $f $OUTDIR/$SUBDIR/$DWIDIR/$d
                ;;                
            *distcorr*)
                printf "Copy sdc data\t${d}\n"
                cp $f $OUTDIR/$SUBDIR/$SDCDIR/$d
                ;;
            *field_mapping*)
                printf "Copy sdc data\t${d}\n"
                cp $f $OUTDIR/$SUBDIR/$SDCDIR/$d
                ;;
        esac
    done
done

mkdir -p -m 777 $OUTDIR/$QCDIR

duration=$SECONDS
printf -v exectime "$(($duration / 60))m:$(($duration % 60))s."
rm -rf dcmlist.txt
# Create filelist for functional processing
ls -d1 ${OUTDIR}/sub-*/${FUNCDIR}/*.nii.gz > ${LOGDIR}/lnifmri_prep_ep2dlist.txt
# Create filelist for anatomical processing
ls -d1 ${OUTDIR}/sub-*/${ANATDIR}/*.nii.gz | grep -v 'mask' > ${LOGDIR}/lnifmri_prep_anatlist.txt
# ls -d1 ${OUTDIR}/sub-*/${ANATDIR}/*mp2rage*.nii.gz > ${LOGDIR}/lnifmri_prep_mp2ragelist.txt
# Create filelist for diffusion processing
# ls -d1 ${OUTDIR}/sub-*/${DWIDIR}/*.nii.gz > ${OUTDIR}/lnifmri_prep_dwilist.txt
# Create filelist for VBM analysis
ls -d1 ${OUTDIR}/sub-*/${ANATDIR}/*.nii.gz  | grep -v 'mask' > ${OUTDIR}/filelist_VBM_template.txt

NextStep