dwi_getPA

#!/bin/bash
#
# Raúl RC
# Febrero 2018
# raulrcruces@inb.unam.mx
#

#------------------------------------------------------------------------------#
# 			FUNCTIONS
help() {
echo " 
Extrae la B0 de la adquisición DWI Postero-Anterior, para generar el fieldmap.

Ejemplo:
	`basename $0` INPUT OUTPUT

		      INPUT   DWI de entrada
		      OUTPUT  Nombre de salida 

Raul RC
INB, Febrero 2018
raulrcruces@inb.unam.mx
"
}

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 2 ]
then
	echo -e "\e[0;31m\n[ERROR]... \tAn argument is missing\n\e[0m \t\tDWI IN: \033[38;5;5m$1\033[0m\n\t\tOut name: \033[38;5;5m$2\033[0m\n"
	help
	exit 0
fi
if [ -f $2 ]; then Error "Output file already exist: $2"; exit 0; fi
if [ ! -f $1 ]; then Error "DWI does not exist: $1"; exit 0; fi


#------------------------------------------------------------------------------#
# 			RUN
echo -e "\033[48;5;58m\n[INIT]..... \tGet the B0 from the PA-DWI with N4 Bias field: $1\n\033[0m"

#------------------------------------------------------------------------------#
# 			VARIABLES
dwi=$1
out=`echo $2 | awk -F "." '{print $1}'`
id=`echo $dwi | awk -F "." '{print $1}'` 
tmp=/tmp/dwiPA_$RANDOM
grad=${tmp}/vectors.b
b0=${tmp}/${id}_b0.nii.gz
n4=${tmp}/${id}_n4.nii.gz

Info "Checking vectors files existence"
for vec in bval bvec; do 
   if ls $id*$vec* 1> /dev/null 2>&1; then
	    test=`ls $id*$vec*`; echo -e "\033[38;5;81m\t\t $test was found \033[0m";
   else
	    Error "$id does not has a $vec file in this directory"; exit 0;
fi
done


bval=`ls $id*bval*`
bvec=`ls $id*bvec*`


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



#------------------------------------------------------------------------------#
# 			Do stuff
Info "Erasing empty rows from gradient table"
empty_row $bvec
empty_row $bval

Info "Getting gradient table "
paste $bvec $bval > $grad
cat $grad

Info "Checking if gradient table is in column format"
vol=`fslval $dwi dim4`
rows=`cat $grad | wc -l`
if [ "$vol" -eq "$rows" ]; then echo -e "YES, the number of rows in $grad and number of volumes in $dwi are the same: $rows"; else Error "Missmatch between gradient-table and VOLUMES in $dwi, check format"; rm -R $tmp; exit 1; fi

Info "Bias Field Correction of $dwi "
cmd "/home/inb/lconcha/fmrilab_software/mrtrix3.git/release/../scripts/dwibiascorrect -grad $grad -ants -force $dwi $n4"

Info "Getting the B0 from $dwi"
cmd "/home/inb/lconcha/fmrilab_software/mrtrix3.git/release/bin/dwiextract -bzero -grad $grad $n4 $out.nii.gz"

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


#------------------------------------------------------------------------------#
# 			End
Info "Outfile: ${out}.nii.gz\n"