mainscrcall_ASL_tag-control-subtraction

#! /bin/bash

# Process tag-control subtraction for ASL files #
# Uses the FSL tool "asl_file"

# Sourcing of functions library files #
. mainscrcall_funclib

# Setting Ctrl + C as key combination to go back to PROCESSING menu. Also signals to the log file (=if there is one) that this script was interrupted
trap "echo -en '\n\nGoing back to the PROCESSING menu '; sleep 2; log_file_scripts_used interrupt; exit" SIGINT

# Checking if variables are not empty
emptvar=${MEDIA}
var_checked="THE MAIN FOLDER HOLDING FMRI DATA"
checkemptvar

emptvar=${EXPERIMENT}
var_checked="THE EXPERIMENT NAME"
checkemptvar

emptvar="${SUBJLIST}"
var_checked="THE SUBJECT(S) TO BE PROCESSED"
checkemptvar

##########			FUNCTIONS USED IN THIS SCRIPT			##########
function tag-control-subtraction_command {
# This function will produce a text file with a list of the commands using "asl_file" to be processed by PPSS

for SUBJ in ${SUBJLIST}
do
	# Creating a subfolder for this subject within the main output folder
	mkdir -p ${asl_output_folder_path}/${SUBJ} 2> /dev/null

	for item in `ls ${asl_mainfolder_path}/${SUBJ}/${modality_folder_name}/${modality_subfolder_name}??_${modality_contrast}/*${inputfile_marker}.nii.gz`
	do
		# Getting only the file name, without extension, into a variable
		file_name_noextension=`echo ${item} | sed 's!'${asl_mainfolder_path}/${SUBJ}/${modality_folder_name}/${modality_subfolder_name}.._${modality_contrast}/'!!g' | sed 's/.nii.gz//'`

		##### Creating the "asl_file" command for PPSS processing #####
		echo -e "asl_file --data=${item} --ntis=${postlabeldelay} --iaf=${data_order} --diff --out=${asl_output_folder_path}/${SUBJ}/${file_name_noextension}_diff --mean=${asl_output_folder_path}/${SUBJ}/${file_name_noextension}_diff_meanperfusion" >> ${temp_folder}/${ppss_command_file}
		###############################################################

		##### Creating a LOG file with the "asl_file" command used for later QA if needed #####
		echo "OS name and version: ${os_nameandversion}; Command: asl_file; FSL `cat $FSLDIR/etc/fslversion`; Date and time: `current_date_time 2`" > ${asl_output_folder_path}/${SUBJ}/LOGFILE_asl_file_tag-control-subtraction_${file_name_noextension}.txt

		echo -e "Command asl_file for doing tag-control subtraction" >> ${asl_output_folder_path}/${SUBJ}/LOGFILE_asl_file_tag-control-subtraction_${file_name_noextension}.txt

		echo -e "\nasl_file --data=${item} --ntis=${postlabeldelay} --iaf=${data_order} --diff --out=${asl_output_folder_path}/${SUBJ}/${file_name_noextension}_diff --mean=${asl_output_folder_path}/${SUBJ}/${file_name_noextension}_diff_meanperfusion" >> ${asl_output_folder_path}/${SUBJ}/LOGFILE_asl_file_tag-control-subtraction_${file_name_noextension}.txt
		###############################################################
	done
done
}

###########################################################################
###############			MAIN MENU ROUTINE			###############
###########################################################################

##### 			VARIABLES TO BE USED IN THIS SCRIPT 		#####
# Assigning a variable to hold the main location of the files generated by this script
temp_folder=/tmp/ppss_tempdir_ASL-tag-control-subtraction # Where the temporary files will be held
ppss_command_file=ASL-tag-control-subtraction_list.txt

# Variables to establish imaging modality
modality_folder_name=rest
modality_subfolder_name=resting
modality_contrast=ASL

asl_mainfolder_path=${SUBJS_FOLDERS_PATH} # Where the subjects folders are. Can be modified by the user in this script.
asl_folder_processed=processed_asl_data # Where the output of ASL-related FSL tools will be saved (within each subjects folder)
asl_output_folder_path=${asl_mainfolder_path}/processed_asl_data
######################################################################

######### Script Main menu - Informing the user what this script does and asking for input #########
clear

# Changing directory to /tmp in case the script comits some error - this will make any commands to be run within /tmp, preventing damage to the file system
cd /tmp

# Removing temporary folders and files created, just in case they were not deleted properly by a previously ran script
rm -r ${temp_folder} 2> /dev/null

# Creating a temporary folder to hold the text file with the subjects to be processed
mkdir ${temp_folder} 2> /dev/null

# Anouncing the purpose of this script
echo -e "###################################"
echo -e "##### TAG-CONTROL SUBTRACTION #####"
echo -e "###################################"

##### GATHERING THE PATH TO THE ANALYSIS FOLDER #####
# FUNCTION CALL: calls the function "analysis_mainfolder" in "mainscrcall_funclib" to allow the user to select the path to the subject's folders
analysis_mainfolder ASL_original

# Assigning the output variable from the function above to a local variable
asl_mainfolder_path=${ANALYSIS_MAINFOLDER_PATH}
######################################################

# Giving instructions to the user
echo
echo -e "This program will process *** TAG-CONTROL SUBTRACTION *** in ASL timeseries files"
echo -e "This will generate:\n1. Tag-control differenced file with (n vols in orig image)/2 volume to be used by \"oxford_asl\" tool;\n2. (relative) perfusion image (same units as the original data)."

echo
echo -e "This processing will be done using the \"asl_file\" tool from FSL"
echo -e "Some initial information is needed prior to processing. Please choose below:"

# While loop for user input
while [ 1 ]
do
	echo
	echo -en "\tData file for input is (1) ORIGINAL or (2) MOTION CORRECTED: "
	read inputfile_origmoco_user

	echo
	echo -en "\tNumber of inversion time(s) (TI)/post-labelling delay(s) (check ASL pulse sequence): "
	read postlabeldelay_user

	echo
	echo -en "\tData order is (1) TAG-CONTROL or (2) CONTROL-TAG: "
	read data_order_user

	echo
	echo -en "\tFULL PATH for the folder to hold ** OUTPUT ** from \"asl_file\" (Hit ENTER for DEFAULT=${asl_output_folder_path}): "
	read asl_output_folder_path_user

	# For Data file for input
	if [ -n "${inputfile_origmoco_user}" ] && [ ${inputfile_origmoco_user} = 1 ]
	then
		inputfile_origmoco_user=original

	elif [ -n "${inputfile_origmoco_user}" ] && [ ${inputfile_origmoco_user} = 2 ]
	then
		inputfile_origmoco_user=motion_corrected
	else
		inputfile_origmoco_user="not entered"
	fi

	# For Data order
	if [ -n "${data_order_user}" ] && [ ${data_order_user} = 1 ]
	then
		data_order_user=tag-control

	elif [ -n "${data_order_user}" ] && [ ${data_order_user} = 2 ]
	then
		data_order_user=control-tag
	else
		data_order_user="not entered"
	fi

	# For output folder path
	if [ -z "${asl_output_folder_path_user}" ]
	then
		# In this case, the user hit ENTER thus it will be used the DEFAULT path
		asl_output_folder_path_user=${asl_output_folder_path}
	fi

	# Asking user's confirmation of data entered
	echo -e "\n"
	echo -e "Information entered:"
	echo -e "\tData file for input: ${inputfile_origmoco_user}"
	echo -e "\tNumber of TI/post label delay: ${postlabeldelay_user}"
	echo -e "\tData order: ${data_order_user}"
	echo -e "\tOutput folder path: ${asl_output_folder_path_user}"

	echo
	echo -en "Is this correct? (y/n) "
	read yesno

	if [ -n "${yesno}" ] && [ ${yesno} = y ]
	then
		# Assigning the values for the variables to be used for processing
		postlabeldelay=${postlabeldelay_user}

		if [ ${data_order_user} = tag-control ]
		then
			data_order=tc

		elif [ ${data_order_user} = control-tag ]
		then
			data_order=ct
		fi

		asl_output_folder_path=${asl_output_folder_path_user}

		break
	else
		echo
		echo -en "Please correct the information entered "

		sleep 1

		# To have a newline between the sentence above and the next (if used in the next, it will make it have 2 newlines)
		echo
	fi
done

# # Based on the user's initial information, now will gather the parameters for "asl_file"
# echo
# echo -e "Gathering now the specific parameters for \"asl_file\""

# ##### ASL acquisition type #####
# # This will influence the TI duration: cASL/pcASL TI=Post Label Delay + Labelling duration; pASL=ost Label Delay only (TI is instantaneous)
# if [ ${acquisition_type_user} = cASL/pcASL ]
# then
# 	echo
# 	echo -en "Enter the total duration for Post label delay + labelling duration in seconds"
# fi

##### Data file for input #####
# This will determine if will use the original ASL timeseries or the motion corrected
if [ ${inputfile_origmoco_user} = original ]
then
	echo
	echo -e "This script will look for a file in this folder:\n${asl_mainfolder_path}/subjID/rest/resting0?_ASL/filename_stdMNI.nii.gz"

	# Assigning the user's decision to a variable
	inputfile_marker=_stdMNI

elif [ ${inputfile_origmoco_user} = motion_corrected ]
then
	echo
	echo -e "*** To use motion corrected ASL timeseries, you must have run MCFLIRT on the original timeseries ***"
	echo -e "This script will look for a file in this folder:\n${asl_mainfolder_path}/subjID/rest/resting0?_ASL/filename_mcf.nii.gz"

	# Assigning the user's decision to a variable
	inputfile_marker=_mcf
fi

echo
echo -e "\t1. Proceed with TAG-CONTROL subtraction"
echo -e "\t0. Back to main menu\n"

# Ask for user input to continue
echo -en "Please enter your option: "
read proceed

while [ 1 ]
do
	case ${proceed} in
	0)
		echo
		echo -en "Going back to the PROCESSING menu "
		sleep 2

		break
		;;
	1)
		# Creating a log file. STEP 1 of 2 = start call
		# Calling the function "log_file_scripts_used" in "functionslibr_FSL" to output the characteristics of this script. It uses 4 parameters: 1. Flag to signal if this function is being called when the calling script starts or when it has finished; 2. The calling script and its purposes (separated by a semicolon); 3. The analysis software type (FSL, Freesurfer) related to the script's use; 4. The tools used (e.g., fsl_motion_outliers, fslreorient2std, etc.)
		log_file_scripts_used start "mainscrcall_ASL_tag-control-subtraction:Perform tag-control subtraction in ASL timeseries" FSL "(tag-control-subtraction_command) asl_file"

		####### MAIN PATH TO SUBJECTS FOLDER CHECK ##############
		# Checking if used the original path to ASL files or the user entered another one ("default_path" variable originates from function "analysis_mainfolder" in "mainscrcall_funclib")
		if [ ${default_path} = yes ]
		then
			# Creating a log file. STEP 1.5 of 2 = midscript call
			# Calling the function "log_file_scripts_used" in "mainscrcall_funclib" to output the characteristics of this script. It uses 4 parameters: 1. Flag to signal if this function is being called when the calling script starts or when it has finished; 2. Reason for midscript call
			log_file_scripts_used midscript "Used the default path for ASL data: ${asl_mainfolder_path}"

		elif [ ${default_path} = no ]
		then
			# Creating a log file. STEP 1.5 of 2 = midscript call
			# Calling the function "log_file_scripts_used" in "mainscrcall_funclib" to output the characteristics of this script. It uses 4 parameters: 1. Flag to signal if this function is being called when the calling script starts or when it has finished; 2. Reason for midscript call
			log_file_scripts_used midscript "Used an alternative path for ASL data: ${asl_mainfolder_path}"
		fi
		#########################################################

		# Giving information to the user on what this script will do
		echo
		echo -e "These are the subjects listed for processing and the respective input file(s):\n"

		# Making the subjects within the "SUBJLIST" variable to be listed in a numbered list for the user
		# Establishing the initial subject numbering
		count=1

		for SUBJ in ${SUBJLIST}
		do
			# This is to add trailing zeros to this number, so instead of "2" you have "002" for example. Maybe needed if subject's listing gets mixed up due to numbers like "10" being listed before "2", e.g. 1 10 11 2 3 4
			counter=`printf "%02d" ${count}`

			echo
			echo "${counter}) ${SUBJ}"

			# Showing the input files
			if [ ${inputfile_marker} = _stdMNI ]
			then
				# Gathering the files available into a variable. Note the use of dots as wildcards for a single character (like "?" in the terminal)
				inputfile_listed=`ls ${asl_mainfolder_path}/${SUBJ}/${modality_folder_name}/${modality_subfolder_name}??_${modality_contrast}/*${inputfile_marker}.nii.gz 2> /dev/null | sed 's!'${asl_mainfolder_path}/${SUBJ}/${modality_folder_name}/${modality_subfolder_name}.._${modality_contrast}/'!!g'`

				# Checking if there are files listed
				if [ -n "${inputfile_listed}" ]
				then
					echo -e "Input files: \n${inputfile_listed}"
				else
					echo -e "Input files: ** None found **"
				fi

			elif [ ${inputfile_marker} = _mcf ]
			then
				# Gathering the files available into a variable. Note the use of dots as wildcards for a single character (like "?" in the terminal)
				inputfile_listed=`ls ${asl_mainfolder_path}/${SUBJ}/${modality_folder_name}/${modality_subfolder_name}??_${modality_contrast}/*${inputfile_marker}.nii.gz 2> /dev/null | sed 's!'${asl_mainfolder_path}/${SUBJ}/${modality_folder_name}/${modality_subfolder_name}.._${modality_contrast}/'!!g'`

				# Checking if there are files listed
				if [ -n "${inputfile_listed}" ]
				then
					echo -e "Input files: \n${inputfile_listed}"
				else
					echo -e "Input files: ** None found **"
				fi
			fi

			# Adding a unit to the numbering variable
			((count++))
		done

		# Cleaning the contents of the variable below
		unset count counter

		# Warning the user about the script assumptions
		echo
		echo -e "*** Please note that this script will use the ASL timeseries files listed above ***"
		echo -e "If they are not correct, you should abort now pressing \"Ctrl + c\""
		echo -en "Otherwise, press any key to continue "
		read -n1 anykey

		# Telling the user that processing will start now
		echo
		echo -e "### Start processing TAG-CONTROL subtraction for all subjects ###"

		# FUNCTION CALL: Calls the function "tag-control-subtraction_command" to produce a text file with a list of the commands using "asl_file" to be processed by PPSS
		tag-control-subtraction_command

		# Checking if there is a PPSS processing file
		if [ -f "${temp_folder}/${ppss_command_file}" ] # Checking if this file exists and is a file
		then
			# Calling the function "parallel_processing_ppss" to run the motion outliers command. Note 4 parameters: 1) path to the folder holding the temporary files for this script; 2) the name of the files holding the commands for PPSS to run; 3) Signal the function "parallel_processing_ppss" that the PPSS log files will be deleted there; 4) Number of parallel processes to be run (empty here, so the function will collected this information).
			parallel_processing_ppss ${temp_folder} ${ppss_command_file} ppss_function

			echo
			echo -e "Finished processing at: `current_date_time 2`"
		else
			echo
			echo -en "*** No PPSS processing file was generated - please check the reason ***"
			echo -en "Press any key to continue "
			read -n1 anykey
		fi

		# Ask for user input to continue
		echo
		echo -en "Press any key to continue to the PROCESSING menu "
		read -n1 anykey

		break
		;;
	*)
		echo -e "No valid option chosen"
		echo -en "Please re-enter an option "

		sleep 2
		;;
	esac
done

# Creating a log file. STEP 2 of 2 = finish call
# Calling the function "log_file_scripts_used" in "functionslibr_FSL" to output the characteristics of this script. It uses 1 parameters: 1. Flag to signal if this function is being called when the calling script starts or when it has finished; 2. List of subjects processed
log_file_scripts_used finish "${SUBJLIST}"

# Removing temporary folders and files created
rm -r ${temp_folder} 2> /dev/null