#!/bin/bash 
set -e

# Requirements for this script
#  installed versions of: FSL5.0.2 or higher , FreeSurfer (version 5 or higher) , gradunwarp (python code from MGH) 
#  environment: use SetUpHCPPipeline.sh  (or individually set FSLDIR, FREESURFER_HOME, HCPPIPEDIR, PATH - for gradient_unwarp.py)

# make pipeline engine happy...
if [ $# -eq 1 ]
then
    echo "Version unknown..."
    exit 0
fi

########################################## PIPELINE OVERVIEW ########################################## 

# TODO

########################################## OUTPUT DIRECTORIES ########################################## 

# TODO

################################################ SUPPORT FUNCTIONS ##################################################

# function for parsing options
getopt1() {
    sopt="$1"
    shift 1
    for fn in $@ ; do
	if [ `echo $fn | grep -- "^${sopt}=" | wc -w` -gt 0 ] ; then
	    echo $fn | sed "s/^${sopt}=//"
	    return 0
	fi
    done
}

defaultopt() {
    echo $1
}

################################################## OPTION PARSING #####################################################

# Just give usage if no arguments specified
if [ $# -eq 0 ] ; then Usage; exit 0; fi

# parse arguments
Path=`getopt1 "--path" $@`  # "$1"
Subject=`getopt1 "--subject" $@`  # "$2"
NameOffMRI=`getopt1 "--fmriname" $@`  # "$6"
LowResMesh=`getopt1 "--lowresmesh" $@`  # "$6"
FinalfMRIResolution=`getopt1 "--fmrires" $@`  # "${14}"
SmoothingFWHM=`getopt1 "--smoothingFWHM" $@`  # "${14}"
GrayordinatesResolution=`getopt1 "--grayordinatesres" $@`  # "${14}"
RUN=`getopt1 "--printcom" $@`  # use ="echo" for just printing everything and not running the commands (default is to run)



# Setup PATHS
PipelineScripts=${HCPPIPEDIR_fMRISurf}
GlobalScripts=${HCPPIPEDIR_Global}
GlobalBinaries=${HCPPIPEDIR_Bin}

#Naming Conventions
AtlasSpaceFolder="MNINonLinear"
T1wFolder="T1w"
NativeFolder="Native"
ResultsFolder="Results"
DownSampleFolder="fsaverage_LR${LowResMesh}k"
ROIFolder="ROIs"
OutputAtlasDenseTimeseries="${NameOffMRI}_Atlas"

AtlasSpaceFolder="$Path"/"$Subject"/"$AtlasSpaceFolder"
T1wFolder="$Path"/"$Subject"/"$T1wFolder"
ResultsFolder="$AtlasSpaceFolder"/"$ResultsFolder"/"$NameOffMRI"
ROIFolder="$AtlasSpaceFolder"/"$ROIFolder"

#Make fMRI Ribbon
#Noisy Voxel Outlier Exclusion
#Ribbon-based Volume to Surface mapping and resampling to standard surface
mkdir -p "$ResultsFolder"/RibbonVolumeToSurfaceMapping
"$PipelineScripts"/RibbonVolumeToSurfaceMapping.sh "$ResultsFolder"/RibbonVolumeToSurfaceMapping "$ResultsFolder"/"$NameOffMRI" "$Subject" "$AtlasSpaceFolder"/"$DownSampleFolder" "$LowResMesh" "$AtlasSpaceFolder"/"$NativeFolder" "$T1wFolder"/"$NativeFolder"

#Surface Smoothing
"$PipelineScripts"/SurfaceSmoothing.sh "$ResultsFolder"/"$NameOffMRI" "$Subject" "$AtlasSpaceFolder"/"$DownSampleFolder" "$LowResMesh" "$SmoothingFWHM"

#Subcortical Processing
"$PipelineScripts"/SubcorticalProcessing.sh "$AtlasSpaceFolder" "$ROIFolder" "$FinalfMRIResolution" "$ResultsFolder" "$NameOffMRI" "$SmoothingFWHM" "$GrayordinatesResolution"

#Generation of Dense Timeseries
"$PipelineScripts"/CreateDenseTimeseries.sh "$AtlasSpaceFolder"/"$DownSampleFolder" "$Subject" "$LowResMesh" "$ResultsFolder"/"$NameOffMRI" "$SmoothingFWHM" "$ROIFolder" "$ResultsFolder"/"$OutputAtlasDenseTimeseries" "$GrayordinatesResolution"