-cd $1
-nbph=`ls -l *0.mhd | wc -l`
-orig=`ls -1 *0.mhd | head -n 1`
-
-cat $orig | sed "s/NDims = .*/NDims = 4/
- s/TransformMatrix = .*/TransformMatrix = 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1/
- /Offset/ s/.*/& 0/
- /CenterOfRotation/ s/.*/& 0/
- s/AnatomicalOrientation = .*/AnatomicalOrientation = ????/
- /ElementSpacing/ s/.*/& 1/
- /DimSize/ s/.*/& $nbph/
- s/ElementDataFile = .*/ElementDataFile = LIST/" > $2
-
-ls -1 *0.raw >> $2
-cd ..
+########## CT #########
+
+list_pattern=""
+list_phase_file=`find $1 -iname "*[0-9].mhd"`
+for phase_file in $list_phase_file
+do
+ phase_file_name=`basename $phase_file`
+ if [[ ! -z `echo "$phase_file_name" | grep ","` ]]
+ then
+ prefix=`echo $phase_file_name | sed "s/,_.*/,_/"`
+ else
+ prefix="NONE"
+ fi
+ if [[ -z `echo "$list_pattern" | grep "$prefix"` ]]
+ then
+ list_pattern="$list_pattern $prefix"
+ fi
+done
+
+
+for pattern in $list_pattern
+do
+
+ if [ "$pattern" = "NONE" ]
+ then
+ pattern=""
+ fi
+
+ nbph=`find $1 -iname "${pattern}*[0-9].mhd" | wc -l`
+ orig=`find $1 -iname "${pattern}*[0-9].mhd" | sort | head -n 1`
+ listph=`find $1 -iname "${pattern}*[0-9].raw" | sort`
+
+ file_name_4D="${pattern}_4D.mhd"
+
+ write_mhd_4D $1
+
+done
+
+
+############ PET ###########
+
+list_pattern=""
+list_phase_file=`find $1 -iname "*[0-9]*\]*.mhd"`
+for phase_file in $list_phase_file
+do
+ phase_file_name=`basename $phase_file`
+ if [[ ! -z `echo "$phase_file_name" | grep "[0-9]-.*\]"` ]]
+ then
+ prefix=`echo $phase_file_name | sed "s/.*[0-9]-/-/;s/\]_.*//"`
+ else
+ prefix="NONE"
+ fi
+ if [[ -z `echo "$list_pattern" | grep -- "$prefix"` ]]
+ then
+ list_pattern="$list_pattern $prefix"
+ fi
+done
+
+
+for pattern in $list_pattern
+do
+
+ if [ "$pattern" = "NONE" ]
+ then
+ pattern=""
+ fi
+
+ nbph=`find $1 -iname "*[0-9]${pattern}\]*.mhd" | wc -l`
+ orig=`find $1 -iname "*[0-9]${pattern}\]*.mhd" | sort | head -n 1`
+ listph=`find $1 -iname "*[0-9]${pattern}\]*.raw" | sort`
+
+ file_name_4D=`basename "$orig" | sed "s/[0-9]${pattern}\]/${pattern}\]/;s/_.mhd/_4D.mhd/"`
+
+ write_mhd_4D $1
+
+done