mainscrcall_structural_analysis

#! /bin/bash

# This script use a FSL tool called "fsl_anat" that provides a general pipeline for processing anatomical images

# 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 MRI DATA"
checkemptvar

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

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

emptvar="${SUBJS_FOLDERS_PATH}"
var_checked="THE FOLDER CONTAINING ALL SUBJECTS' FOLDERS"
checkemptvar

##########			FUNCTIONS USED IN THIS SCRIPT			##########
function structural_fslanat {
# This function will check if the subjects listed have the ANATOMICAL file with the contrast chosen by user, and if so add them to the PPSS processing file

# Count how many valid files there are
# Establishing the initial numbering
count_subj=0
count_valid_file=0

for SUBJ in ${SUBJLIST}
do
	# Checking if this subject has a ANATOMICAL file with the contrast chosen by user
	# First gathering the anatomical file for the subject
	subj_anat_file_fullpath=`ls ${SUBJS_FOLDERS_PATH}/${SUBJ}/${anat_folder}/*_${CONTRAST_PROCESS}*_orig.nii.gz`

	# Checking if this a valid file
	if [ -s "${subj_anat_file_fullpath}" ] # Checks if a file exists and it is not empty. MUST HAVE THE PARENTHESIS OTHERWISE THE TEST STILL GIVER "TRUE" EVEN IF THE VARIABLE IS EMPTY.
	then
		# Gathering the ANATOMICAL file name withou the full path
		subj_anat_file_nameonly=`echo ${subj_anat_file_fullpath} | awk -F/ '{print $NF}'`

		# Giving feedback to the user
		echo
		echo -e "Subject ID: ${SUBJ} - ANATOMICAL file: ${subj_anat_file_nameonly}"

		# COMMAND FOR PPSS: Adding this subject's ANATOMICAL file to the PPSS processing file. Note the use of the option "-t" and the variable CONTRAST_PROCESS to tell fsl_anat which type of ANATOMICAL will be processed
		# If the input image is not T1-weighted, fsl_anat demands that the flags "--nononlinreg" and "--nosubcortseg" NOT be used, since it is not possible to do non-linear registration with nono-T1 images
		if [ X${CONTRAST_PROCESS} = XT1 ]
		then
			echo "fsl_anat -t ${CONTRAST_PROCESS} -i ${subj_anat_file_fullpath}" >> ${temp_folder}/${ppss_command_file}
		else # In this case the image ins not T1, so it will make the call to fsl_anat with the flag
			echo "fsl_anat -t ${CONTRAST_PROCESS} --nononlinreg --nosubcortseg -i ${subj_anat_file_fullpath}" >> ${temp_folder}/${ppss_command_file}
		fi

		# Adding a unit to the numbering variable
		((count_valid_file++))

		##### Creating a LOG file with the commands used for later QA if needed #####
		echo "OS name and version: ${os_nameandversion}; Command: fsl_anat; FSL `cat $FSLDIR/etc/fslversion`; Date and time: `current_date_time 2`" > ${SUBJS_FOLDERS_PATH}/${SUBJ}/${anat_folder}/LOGFILE_fslanat_${subj_anat_file_nameonly}.txt

		echo -e "Command fsl_anat that provides a general pipeline for processing anatomical images" >> ${SUBJS_FOLDERS_PATH}/${SUBJ}/${anat_folder}/LOGFILE_fslanat_${subj_anat_file_nameonly}.txt

		if [ X${CONTRAST_PROCESS} = XT1 ]
		then
			echo -e "\nfsl_anat -t ${CONTRAST_PROCESS} -i ${subj_anat_file_fullpath}" >> ${SUBJS_FOLDERS_PATH}/${SUBJ}/${anat_folder}/LOGFILE_fslanat_${subj_anat_file_nameonly}.txt
		else # In this case the image ins not T1, so it will make the call to fsl_anat with the flag
			echo -e "\nfsl_anat -t ${CONTRAST_PROCESS} --nononlinreg --nosubcortseg -i ${subj_anat_file_fullpath}" >> ${SUBJS_FOLDERS_PATH}/${SUBJ}/${anat_folder}/LOGFILE_fslanat_${subj_anat_file_nameonly}.txt
		fi
		###############################
	else
		# Giving feedback to the user
		echo
		echo -e "Subject \"${SUBJ}\" does not have a valid ANTOMICAL file for contrast \"${CONTRAST_PROCESS}\""
		echo -e "This subject will not be processed"

		echo
		echo -en "Press any key to continue"
		read -n1 anykey
	fi

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

# Giving final feedback to the user on the number of files valid and number of subjects
echo
echo -e "Please check the number of subjects listed and ANATOMICAL files below:"
echo -e "${count_subj} = Number of subjects listed for processing"
echo -e "${count_valid_file} = Number of valid ANATOMICAL files with contrast *** ${CONTRAST_PROCESS} ***"

echo
echo -e "The above numbers should be the same, if all subjects listed are to be processed now"
echo -e "If this is not true, please check the reasons why before processing (press Ctrl + C to go back to the PROCESSING menu)"

echo
echo -en "If you want to continue processing, press any key "
read -n1 anykey
}

function structural_brain_atrophy {
# This function will estimate brain atrophy using SIENA/SIENAX

# Asking the user to which tool will be used: SIENA or SIENAX
echo
echo -e "Do you want to run:"
echo -e "1. SIENA (longitudinal 2-timepoint estimation)"
echo -e "2. SIENAX (cross sectional single-timepoint estimation) ~12min per image"

echo
echo -en "Please enter your option here: "
read tool_choosen

# Checking the user option
if [ -n "${tool_choosen}" ] && [ ${tool_choosen} = 1 ] # Checking if this variable is not empty and equal to "1"
then
	echo -e "\n"
	echo -e "*** UNDER CONSTRUCTION ***"

	echo
	echo -en "Press any key to go back to the PROCESSING menu "
	read -n1 any key

	exit

elif [ -n "${tool_choosen}" ] && [ ${tool_choosen} = 2 ] # Checking if this variable is not empty and equal to "2"
then
	while [ 1 ]
	do
		# Allowing the use to choose the options for SIENAX
		echo -e "\n"
		echo -e "Please choose from the options below:"
		echo -e "\t1. Use reoriented ANATOMICAL (images reoriented to MNI; default is original image)"
		echo -e "\t2. SIENAX: Debug (No deletion of intermediate files)"
		echo -e "\t3. SIENAX: Regional volume estimation (peripheral GM and ventricular CSF)"
		echo -e "\t4. SIENAX: BET options (enter custom options for brain extraction)"
		echo -e "\t5. SIENAX: FAST options (enter custom options for brain segmentation)"

		echo
		echo -en "Please enter your option here (If more than one, separate by space): "
		read options_sienax_chosen

		# Making the options "options_sienax_chosen" variable to be listed in a numbered list for the user
		if [ -n "${options_sienax_chosen}" ] # Checking if this variable is non-zero in length
		then
			# Establishing the initial numbering
			count=1

			# Collecting the metrics listed in the "metric_choose" variable into another variable to be used in the FUNCTION "NUMBERED_LIST" (functionslibr_FSL)
			var1_available=`for options_sienax_item in ${options_sienax_available}; do echo "${count}=${options_sienax_item}"; ((count++)); done` # variable with all the files in a numbered list
			var2_list="${options_sienax_chosen}" # The numbers chosen by the user corresponding to the files to be used

			# Calling the function "numbered_list_display" to present the anatomical files available in a numbered list to the user. Note the parameters to be passed on to the function
			numbered_list_display "${var1_available}" "${var2_list}"

			# Retrieving the results of the function above from the variable "files_to_use" into a variable to be used by the present script
			options_sienax_chosen="${files_to_use}"

			# Cleaning the contents of the variables below
			unset files_to_use count

			# Showing to the user the option entered prior to processing
			echo -e "\n"
			echo -e "These are the options entered for SIENAX processing:\n"

			# Listing the options to be listed in a numbered list for the user
			# Establishing tne initial numbering
			count=1

			for item in ${options_sienax_chosen}
			do
				echo "${count}) ${item}"

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

			# Cleaning the contents of the numbering variable
			unset count

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

			if [ ${yesno} = y ] || [ ${yesno} = Y ]
			then
				##### Consolidating the options chosen by user into a variable #####
				OPTIONS_SIENAX=${options_sienax_chosen}

				# Going to the processing stage
				break

			elif [ ${yesno} = n ] || [ ${yesno} = N ]
			then
				echo -e "\n"
				echo -en "Please correct the options to be used "

				sleep 2

				# Cleaning the contents of the variable below
				unset options_sienax_chosen
			fi

		elif [ -z "${options_sienax_chosen}" ] # Checking if this variable is zero in length. In this case, it will use the default metric
		then
			echo
			echo -e "*** No option was choosen ***"
			echo -e "SIENAX will run with DEFAULT options\n"

			echo -en "Press any key to continue "
			read -n1 anykey

			##### Consolidating the options chosen by user into a variable #####
			OPTIONS_SIENAX=""
		fi
	done

	# Establishing the options for SIENAX command line
	# Checking if the user chose options or if the variable is empty
	if [ -n "${OPTIONS_SIENAX}" ] # Checking if it is not empty
	then
		# Variable holding the SIENAX options for command line
		command_options_sienax=""

		for item in ${OPTIONS_SIENAX}
		do
			# Checking the item being processed to give the option required
			if [ ${item} = reoriented_images ]
			then
				anat_orig_reoriented=stdMNI.nii.gz

			elif [ ${item} = debug ]
			then
				command_options_sienax="${command_options_sienax} -d"

			elif [ ${item} = regional_volume_estimation ]
			then
				command_options_sienax="${command_options_sienax} -r"

			elif [ ${item} = bet_options ]
			then
				# Asking the user what BET options he wants to use
				while [ 1 ]
				do
					echo
					echo -en "Please enter the BET options to modify (see BET wiki for list of options): "
					read bet_options_mod_user

					echo -e "\n"
					echo -e "You entered the following BET options: ${bet_options_mod_user}"

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

					# Checking if the user accepts the info presented
					if [ -n "${yesno}" ] && [ "${yesno}" = y ] || [ "${yesno}" = Y ] # Checking if this variable is not empty and it is equal to yes
					then
						# Accepting the BET options entered
						command_options_sienax="${command_options_sienax} -B \"${bet_options_mod_user}\""

						break

					elif [ -n "${yesno}" ] && [ "${yesno}" = n ] || [ "${yesno}" = N ] # checking if this variable is not empty and it is equal to no
					then
						echo -e "\n"
						echo -en "Please correct the options entered "

						sleep 2
					else
						echo -e "\n"
						echo -en "No response was detected. You must choose yes or no "

						sleep 2
					fi
				done

			elif [ ${item} = fast_options ]
			then
				# Asking the user what FAST options he wants to use
				while [ 1 ]
				do
					echo
					echo -en "Please enter the FAST options to modify (see FAST wiki for list of options): "
					read fast_options_mod_user

					echo -e "\n"
					echo -e "You entered the following BET options: ${fast_options_mod_user}"

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

					# Checking if the user accepts the info presented
					if [ -n "${yesno}" ] && [ "${yesno}" = y ] || [ "${yesno}" = Y ] # checking if this variable is not empty and it is equal to yes
					then
						# Accepting the BET options entered
						command_options_sienax="${command_options_sienax} -S \"${fast_options_mod_user}\""

						break

					elif [ -n "${yesno}" ] && [ "${yesno}" = n ] || [ "${yesno}" = N ] # Checking if this variable is not empty and it is equal to no
					then
						echo -e "\n"
						echo -en "Please correct the options entered "

						sleep 2
					else
						echo -e "\n"
						echo -en "No response was detected. You must choose yes or no "

						sleep 2
					fi
				done
			fi
		done

	elif [ -z "${OPTIONS_SIENAX}" ]
	then
		# Variable with SIENAX options empty
		command_options_sienax=""
	fi

	# Checking if this image is T2-weighted - SIENAX needs an specific option for that
	if [ ${CONTRAST_PROCESS} = T2 ]
	then
		command_options_sienax="${command_options_sienax} -t2"
	fi

	# Count how many valid files there are
	# Establishing the initial numbering
	count_subj=0
	count_valid_file=0

	for SUBJ in ${SUBJLIST}
	do
		# Checking if this subject has a ANATOMICAL file with the contrast chosen by user
		# First gathering the ANATOMICAL file for the subject
		subj_anat_file_fullpath=`ls ${SUBJS_FOLDERS_PATH}/${SUBJ}/${anat_folder}/*_${CONTRAST_PROCESS}*_${anat_orig_reoriented}`

		# Checking if this a valid file
		if [ -s "${subj_anat_file_fullpath}" ] # Checks if a file exists and it is not empty. MUST HAVE THE PARENTHESIS< OTHERWISE THE TEST STILL GIVER "TRUE" EVEN IF THE VARIABLE IS EMPTY.
		then
			# Gathering the ANATOMICAL file name withou the full path
			subj_anat_file_nameonly=`echo ${subj_anat_file_fullpath} | awk -F/ '{print $NF}'`

			# Giving feedback to the user
			echo
			echo -e "Subject ID: ${SUBJ} - ANATOMICAL file: ${subj_anat_file_nameonly}"

			# COMMAND FOR PPSS: Adding this subject's ANATOMICAL file to the PPSS processing file
			echo "sienax ${subj_anat_file_fullpath} ${command_options_sienax}" >> ${temp_folder}/${ppss_command_file}

			# Adding a unit to the numbering variable
			((count_valid_file++))

			##### Creating a LOG file with the commands used for later QA if needed #####
			echo "OS name and version: ${os_nameandversion}; Command: sienax; FSL `cat $FSLDIR/etc/fslversion`; Date and time: `current_date_time 2`" > ${SUBJS_FOLDERS_PATH}/${SUBJ}/${anat_folder}/LOGFILE_sienax_${subj_anat_file_nameonly}.txt

			echo -e "Command sienax to perform analysis of brain change, in particular, the estimation of atrophy using anatomical images" >> ${SUBJS_FOLDERS_PATH}/${SUBJ}/${anat_folder}/LOGFILE_sienax_${subj_anat_file_nameonly}.txt

			echo -e "\nsienax ${subj_anat_file_fullpath} ${command_options_sienax}" >> ${SUBJS_FOLDERS_PATH}/${SUBJ}/${anat_folder}/LOGFILE_sienax_${subj_anat_file_nameonly}.txt
			###############################
		else
			# Giving feedback to the user
			echo
			echo -e "Subject \"${SUBJ}\" does not have a valid ANTOMICAL file for contrast \"${CONTRAST_PROCESS}\""
			echo -e "This subject will not be processed"

			echo
			echo -en "Press any key to continue"
			read -n1 anykey
		fi

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

	# Giving final feedback to the user on the number of files valid and number of subjects
	echo
	echo -e "Please check the number of subjects listed and ANATOMICAL files below:"
	echo -e "${count_subj} = Number of subjects listed for processing"
	echo -e "${count_valid_file} = Number of valid ANATOMICAL files with contrast *** ${CONTRAST_PROCESS} ***"

	echo
	echo -e "The above numbers should be the same, if all subjects listed are to be processed now"
	echo -e "If this is not true, please check the reasons why before processing (press Ctrl + C to go back to the PROCESSING menu)"

	echo
	echo -en "If you want to continue processing, press any key "
	read -n1 anykey
fi
}

###########################################################################
###############			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
ppss_command_file=subject_structural_processing

struct_contrast_available="T1 T2 PD" # Contrasts for ANATOMICAL images available
anat_folder=anat # The name of the folder holding the ANATOMICAL images
anat_orig_reoriented=orig.nii.gz

options_sienax_available="reoriented_images debug regional_volume_estimation bet_options fast_options"
######################################################################

# 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

# MODIFY THIS SCRIPT TO DO EITHER FSL_ANAT OR SIENA/SIENAX PROCESSING

# Giving feedback to the user
echo -e "#####################################################################"
echo -e "\tThis program will process ANATOMICAL images for structural analysis"
echo -e "######################################################################"

# Showing the subjects to be processed here to the user
echo
echo -e "ANATOMICAL files will be processed here for the following subjects:\n"

# Making the subjects within the "SUBJLIST" variable to be listed in a numbered list for the user
# Establishing the initial 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 "${counter}) ${subj}"

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

# Cleaning the contents of the numbering variable
unset count

######### Script Main menu - Informing the user what this script does and asking for input #########
while [ 1 ]
do
	echo
	echo -e "This program allows to: 1. Process ANATOMICAL images using \"fsl_anat\"; and 2. Do brain atrophy estimation using \"SIENA/SIENAX\"\n"

	echo -e "Do you want to use:"
	echo -e "\t1) \"fsl_anat\": ** ANATOMICAL images processing **"
	echo -e "\t2) \"SIENA/SIENAX\": ** Estimation of brain atrophy **"
	echo -e "\t0. Back to main menu\n"

	echo -en "Please enter your option here: "
	read main_option

	case ${main_option} in
	0)
		echo
		echo -en "Going back to the PROCESSING menu "
		sleep 2

		exit
		;;
	1)
		echo -e "\n"
		echo -e "Starting ANATOMICAL processing pipeline using \"fsl_anat\""

		# FUNCTION CALL: Calling function "anatomical_contrast" in "mainscrcall_funclib" to allow the user to choose the contrast in the anatomical images to be processed
		anatomical_contrast

		# 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.) preceeded by the script's function that calls it in parenthesis
		log_file_scripts_used start "structural_analysis:ANATOMICAL images processing pipeline using the FSL tool \"fsl_anat\"" FSL "(structural_fslanat) fsl_anat"

		# FUNCTION CALL: Calling function "structural_fslanat" to select which ANATOMICAL files will be processed
		structural_fslanat

		# Calling the function "parallel_processing_ppss" to run the command. Note 2 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. Added a 3rd parameter to signal the function "parallel_processing_ppss" that the PPSS log files will be deleted there.
		# Not using the 4th parameter (list of unique identifiers for differentiating commands, e.g. a list of subjects), SO ALL SUBJECT'S FILES ARE PROCESSED IN A ROW, INSTEAD OF ON A SUBJECT-BY-SUBJECT BASIS (FASTER AND OPTIMIZED USE OF PPSS).
		parallel_processing_ppss ${temp_folder} ${ppss_command_file} ppss_function

		break
		;;
	2)
		echo -e "\n"
		echo -e "Starting brain atrophy estimation using \"SIENA/SIENAX\""

		# FUNCTION CALL: Calling function "anatomical_contrast" in "mainscrcall_funclib" to allow the user to choose the contrast in the anatomical images to be processed
		anatomical_contrast

		# 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.) preceeded by the script's function that calls it in parenthesis
		log_file_scripts_used start "structural_analysis:Brain atrophy estimation using \"SIENA/SIENAX\"" FSL "(structural_brain_atrophy) SIENA/SIENAX"

		# FUNCTION CALL: Calling function "structural_brain_atrophy" to assess brain atrophy using SIENA/SIENAX
		structural_brain_atrophy

		# Calling the function "parallel_processing_ppss" to run the command. Note 2 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. Added a 3rd parameter to signal the function "parallel_processing_ppss" that the PPSS log files will be deleted there.
		# Not using the 4th parameter (list of unique identifiers for differentiating commands, e.g. a list of subjects), SO ALL SUBJECT'S FILES ARE PROCESSED IN A ROW, INSTEAD OF ON A SUBJECT-BY-SUBJECT BASIS (FASTER AND OPTIMIZED USE OF PPSS).
		parallel_processing_ppss ${temp_folder} ${ppss_command_file} ppss_function

		break
		;;
	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