dwi_vec

#!/bin/bash


#------------------------------------------------------------------------------#
# 			FUNCTIONS
help() {
echo " 
Corrige los vectores de difusión asociados a la direccion (bvecs) en caso de que la adquisición tenga una rotación (si fue procesado con PAR/REC de Philips Achieva TX 3).
Y en caso de que sean más de dos DWI las concatena en un solo arhivo.

FALTA LA CONDICION PARA CUANDO SOLO HAY UN DWI linea 114 y 162

Realizará los siguientes pasos:
	1.Obtener la matriz de rotación. 
	  Para los archivos PAR/REC es el archivo '.omat' que se obtienes tras usar PARconv_v1.12.sh
	  omat es un archivo de texto que representa una matriz de 4x4 
	2.Rotar los vectores. 
	  Multiplicación de los vectores bvecs por la matriz omat
	3. Concatena  en el orden dado
	3.Invertir Y y Z de los bvecs. 
	  Multiplica por -1 la coordenada Y & Z de los bvecs.

Ejemplo:
	`basename $0` -in \"DWI_01.nii.gz DWI_02.nii.gz\" -out DWI_outname.nii.gz

		      -in DWIs para corregir y concatenar
		      -out Nombre de salida 

Raul RC
INB, Febrero 2018
raulrcruces@inb.unam.mx
"
}
#---------------- FUNCTION: Erase EMPTY ROWS ----------------#
empty_row() {
Txt=$1
c=`grep -c "^\s*$" $Txt`
if ((c > 0)); 
then
	echo  -e "\033[38;5;83m\n[INFO]... Borrando filas en blanco de $Txt \033[0m"
	sed -i '/^\s*$/d' $Txt
fi
}

#---------------- FUNCTION: PRINT COLOR COMMAND ----------------#
cmd() {
text=$1
echo -e "\033[38;5;208mcommand--> $text \033[0m"
echo $($text)
}

Info() {
Col="38;5;83m" # Color code 
echo  -e "\033[$Col\n[INFO]..$1 \033[0m"
}

Error() {
echo -e "\e[0;31m\n[ERROR]..... $1\n\e[0m"
}

#------------------------------------------------------------------------------#
# 			WARNINGS
# Number of inputs
if [ $# -lt 4 ]; then Error "Some arguments are missing"; help; exit 0; fi
if [ $# -gt 4 ]; then Error "Too may arguments, please quote between DWIs:\n\t\t\"dwi01.nii.gz dwi02.nii.gz dwi03.nii.gz\""; help; exit 0; fi



#------------------------------------------------------------------------------#
# 			ARGUMENTS
echo -e "\033[48;5;58m\n[INIT]..... \tDWI Vector Correction for Philips Achieva TX\n\033[0m"
for arg in "$@"
do
  case "$arg" in
  -h|-help)
    help
    exit 1
  ;;
  -out)
   out=`echo $2 | awk -F "." '{print $1}'` 
   Info "Output ID:\t\033[0m\033[38;5;81m$out\033[0m"
   shift;shift
  ;;
  -in)
   in=$2
   Info "Inputs are:\t\033[0m\033[38;5;81m$in\033[0m"
   arr=($in)
   shift;shift
  ;;
   esac
done
if [ -f $out.nii.gz ] ; then Error "Output file already exist: $out.nii.gz"; exit 0; fi


#------------------------------------------------------------------------------#
# 			VARIABLES
dwis=""
tmp=/tmp/vectorCorr_$RANDOM

# Temporal directory
Info "Temporal directory"
cmd "mkdir $tmp"

# Checks the existence of the volume
Info "Checking volumes existence:"
for var in ${arr[@]}; do
	if [ ! -f $var ]; then Error "$var was not found, skiping"; id=""; else
	echo -e "\033[38;5;81m\t\t $var was found \033[0m"; id=`echo $var | awk -F "." '{print $1}'` 
	dwis="$dwis $id"	
	fi
done
# Array of variables
dwis=($dwis)
Ndwi=${#dwis[@]}
Info "Number of SHELLS: $Ndwi"
if [ "${Ndwi}" -lt 1 ]; then 
	Error "Not enough inputs to work, please check the names of your DWIs"; rm-Rf $tmp; exit 0; else
	Info "We have ${#dwis[@]} DWIs to work:"
	echo -e "\t\t\033[38;5;81m ${dwis[@]} \033[0m" 

fi



#------------------------------------------------------------------------------#
# 			EMPTY ROWS in VECTORS FILES
N=0
Info "Checking vectors files existence"
for nii in ${dwis[@]}; do
	for vec in bval bvec; do 
	if ls $nii*$vec* 1> /dev/null 2>&1; then
	    dwi=`ls $nii*$vec*`; echo -e "\033[38;5;81m\t\t $dwi was found \033[0m";
	    empty_row $dwi 
	else
	    Error "$nii does not has BVECS here"; N=1;
	fi
	done
done
if [ "${N}" == 1 ]; then Error "A VECTOR file is missing"; exit 0; fi



#------------------------------------------------------------------------------#
# 			Orientation and Number of vectors
Info "Checking bvecs orientarion and number of directions"
bvals=""
bvecs=""
DWIs=""
for nii in ${dwis[@]}; do
	for vec in bvec; do bve=`ls $nii*$vec*`; bva=`ls $nii*bval*`;
# Count the number of columns of bvecs
	Ncol=`awk '{print NF}' ${bve} | sort -nu | tail -n 1`
	if [ "$Ncol" != 3 ]; then echo -e "\033[38;5;81m\t\t $bve has $Ncol columns, it will be transpose \033[0m"; transpose $bve; transpose $bva; fi
# Count the number of columns of bvecs
	Nrow=`cat ${bve} | wc -l`
	if [ "$Nrow" -lt 6 ]; then Error "${nii} does not have enought directions, please remove it"; exit 0; else 
	echo -e "\033[38;5;81m\t\t ${bve} has $Nrow directions \033[0m"; bvals="$bvals $bva"; bvecs="$bvecs $bve"; DWIs="$DWIs $nii.nii.gz" ;fi
	done
done


#------------------------------------------------------------------------------#
# 			Concatenate DWIs

if [ "${Ndwi}" -gt 1 ]; then Info "Concatenation of DWIs"
cmd "/home/inb/lconcha/fmrilab_software/mrtrix3.git/release/bin/mrcat -axis 3 $DWIs $out.nii.gz"
else
Info "Input DWIs is the same as the output"
cmd "cp $DWIs $out.nii.gz"
fi

#------------------------------------------------------------------------------#
# 			Concatenate vectors & Inverted for philips
Bvec="$out.bvecs"
Bval="$out.bvals"
Info "Concatenation of bvals"
echo -e "\033[38;5;81m\t\t bvals = $bvals\033[0m"
cat $bvals > $Bval

Info "Concatenation of bvecs and Philips Achieva Tx 3.0T correction (Y,Z*-1)"
echo -e "\033[38;5;81m\t\tbvecs = $bvecs\033[0m"
cat $bvecs | awk '{print $1,-$2,-$3}' > $Bvec


#------------------------------------------------------------------------------#
# 			Rotate bvecs if omat exist
if [ -d omat ]; then Info " Rotating bvecs according to the adquisition matrix: ${dwis[0]}_to0.omat"; 
echo -e "\033[38;5;81m\t\tI assume that all omats are the same please CHECK\033[0m";
	trans=omat/${dwis[0]}_to0.omat
	rot=${tmp}/bvecs_rotated.txt
	cmd "xfmrot $trans $Bvec $rot"
	cmd "mv $rot $Bvec"
else
Info "No other rotations are needed for the bvecs"
fi


#------------------------------------------------------------------------------#
# 			Removes Temoral Files
Info "Deleting temporal files"
cmd "rm -R $tmp"

#------------------------------------------------------------------------------#
# 			Number of BVECS and DWI volumes
Nvec=`cat $Bvec | wc -l`
Ndir=`/home/inb/lconcha/fmrilab_software/mrtrix3.git/release/bin/mrinfo -size $out.nii.gz | awk -F " " '{print $4}'`
if [ "$Ndir" != "$Nvec" ]; then echo -e "\e[0;31m\n[WARNING]..... Missmatch between NUMBER of Volumes ($Ndir) and bvecs ($Nvec)\n\t\tTRY removing MEAN-DWI volumes\n\e[0m"; exit 0; else Info "Number of bvecs: $Nvec.  Number of DWI volumes: $Ndir"; fi