dicomdir_to_nifti

#!/bin/tcsh -f

#
#	Initialise values
#
set name_protocol = ()
set nifti_file_name = ()
set targetDir = ()
set PrintHelp = 0

if ( $#argv == 0 ) goto usage_exit;

set n = `echo "$argv" | grep -e -help | wc -l` 
if ( $n != 0 ) then
	set PrintHelp = 1
	goto usage_exit
endif

goto parse_args
parse_args_return:

goto check_params
check_params_return:

if ( ! -d ${targetDir} ) then
	echo "Error: target directory $targetDir does not exist"
	exit 1
endif

#set temp_nifti_dir = /var/tmp/temp_dir$$
set temp_nifti_dir = temp_dir$$
mkdir -p $temp_nifti_dir

#
#	Loop through subjects
#
@ nth = 0
set subject_list = `ls`
foreach subject ( $subject_list )

	if ( ${subject} == ${temp_nifti_dir} ) then
		continue
	endif
	set n = `echo "$subject" | grep -e native_ | wc -l`
	if ( $n == 1 ) then
		continue
	endif

	echo
	echo $subject

	set found_dir = ()
	set dir_list = `ls $subject`
	foreach dir ($dir_list )
		if ( -f $dir ) then
			continue
		endif

#echo "dir = $dir"

		set n = `echo "$dir" | grep -e $name_protocol | wc -l`
		if ( $n == 1 ) then
			set found_dir = $dir
			break;
		endif
	end

#echo "found_dir = $found_dir"

	if ( $#found_dir == 0 ) then
		echo "Warning: requested directory does not exist for subject $subject"
		continue
	endif

#continue

	dcm2nii -o ${temp_nifti_dir} ${subject}/${found_dir}
	mv ${temp_nifti_dir}/*.nii.gz ${targetDir}/${subject}_${nifti_file_name}

	fslinfo ${targetDir}/${subject}_${nifti_file_name}

#exit 1
end

rm -d ${temp_nifti_dir}

echo "Finished"
issue_beep

date

exit 0

###############################################

############--------------##################
parse_args:
set cmdline = ($argv)
while ( $#argv != 0 )

	set flag = $argv[1]; shift
  
	switch( $flag )

		case "-scan_protocol":
			if ( $#argv < 1 ) goto arg1err
			set name_protocol = "$argv[1]"; shift
		breaksw

		case "-name":
			if ( $#argv < 1 ) goto arg1err
			set nifti_file_name = "$argv[1]"; shift
		breaksw

		case "-targ":
			if ( $#argv < 1 ) goto arg1err
			set targetDir = "$argv[1]"; shift
		breaksw

		default:
			echo ERROR: Flag $flag unrecognised. 
			echo $cmdline
			exit 1
		breaksw

	endsw

end

goto parse_args_return

############--------------##################

############--------------##################
check_params:

if ( $#name_protocol == 0 ) then
	echo "ERROR: must specify name of scan protocol"
	exit 1
endif

if ( $#nifti_file_name == 0 ) then
	echo "ERROR: must specify name of converted nifti"
	exit 1
endif

if ( $#targetDir == 0 ) then
	echo "ERROR: must specify name of target directory"
	exit 1
endif

goto check_params_return
############--------------##################

############--------------##################
arg1err:
	echo "ERROR: flag $flag requires one argument"
	exit 1
############--------------##################

############--------------##################
arg2err:
	echo "ERROR: flag $flag requires two arguments"
	exit 1
############--------------##################

############--------------##################
usage_exit:
	set tool_name = `basename $0`
	echo ""
	echo "$tool_name"
	echo ""
	echo "Working directory should be directory which holds the subject directories containing the DICOM directories"
	echo ""
	echo "Required Arguments:";
	echo "   -scan_protocol <name of scan protocol> : name of scan protocol which should be prersent in name of DICOM directory"
	echo "   -name <file name> : name of converted NIFTI file (subject name will be included at start of each name)"
	echo "   -targ targetdir : name of directory to which the nifti file will be written"
	echo ""
	echo "Other Arguments"
	echo "   -help"
	echo ""

	if (! $PrintHelp ) exit 1

	cat $0 | awk 'BEGIN{prt=0}{if(prt) print $0; if($1 == "BEGINHELP") prt = 1 }'

exit 1


#---- Everything below here is printed out as part of help -----#
BEGINHELP

Tool to convert DICOM directory to named NIFTI file for all subjects.
Used is dcm2nii to convert dicom files to NIFTI