extractBetas

#!/bin/bash
#extractBetas
#The extractBetas script is intended to extract particular coefficients of interest from
#level 1 statistics files for each subject and to place the sub-brick files into a single
#level 2 statistics directory for further analysis (e.g., 3dANOVA2).
#
#The program expects you to pass in a configuration file using -c that defines the directories to
#be processed, the output directory, sub-bricks to be extracted, 
#and naming convention for the statistics files. See the example config file.
#
#example call: sh extractBetas.sh -c ~/fMRIStudy1/Study1_extractBetas.cfg
#
#Author: Michael Hallquist
#Written: 5/1/2010
#Last updated: 7/25/2011
#
#Changelog:
#7/25/2011:
# - Prior version was deleting all BRIK and HEAD files in the directory to make sure that 3dcalc command succeeded.
#     Better is to use -overwrite for 3dcalc, which preserves any needed files in the dir.

#parse -c option for config file
while getopts c: option
do
    case "$option" in
	c) configfile=$OPTARG ;;
    esac
done

if [ -z "$configfile" ]; then
    echo "Config file not specified. Please pass using the -c parameter"
    exit 1
fi

#check that the config file exists
if [ ! -f $configfile ]
then
    echo "Config file (-c) could not be found: $configfile"
    exit 1
else
    echo "Config file: $configfile"
    . $configfile #source the config file, importing the values into this script context
fi

if [ ! -d $baseDir ]
then
    echo "Base directory does not exist. Quitting program."
    exit 1
fi

if [ ! -d $outputDir ]
then
    echo "Output directory does not exist. Creating: $outputDir"
    mkdir -p $outputDir #-p creates any missing parent directories
fi

#check that required arguments are defined in the config file.
if [ -z "$statsDir" ]; then
    echo "statsDir must be defined in the config file."
    exit 1
fi

if [ -z "$subBricks" ]; then
    echo "subBricks must be defined in the config file."
    exit 1
fi

if [ -z "$statsFilePrefix" ]; then
    echo "statsFilePrefix must be defined in the config file."
    exit 1
fi

if [ -z "$subjectDirs" ]; then
    echo "subjectDirs must be defined in the config file."
    exit 1
fi


count=${#subjectDirs[@]}
#echo "count = $count"

#using ${subjectDirs[@]} makes the program see each element as a separate word
#${subjectDirs[*]} treats all as the same word

for subject in ${subjectDirs[@]}
do
    echo "Extracting sub-bricks for subject: $subject"
    thisDir=${baseDir}/${subject}/${statsDir}
    if [ ! -d "$thisDir" ]; then
	echo "Subject directory does not exist: $thisDir"
	exit 1
    fi

    cd $thisDir 

    #run 3dcalc to extract sub-bricks

    #Create an empty array for all possible sub-brick suffixes (for selecting the right files with mv)
    #reinitialize to empty for each iteration (otherwise expands with each subject)
    subBrickNames=()

    #extract sub-bricks
    #need quotes around the array to ensure that bash doesn't reinterpret
    #the array as a flat series of words (i.e., we want to retain the pairs)
    for subBrick in "${subBricks[@]}"
    do
	#echo "subBrick: $subBrick"
	#echo "first param: $1"
	#echo "second param: $2"

    	set -- $subBrick #parse the numeric position and sub-brick names into $1 and $2, respectively
    	3dcalc -overwrite -a "${statsFilePrefix}[$1]" -expr a -prefix ${subject}_$2
    	subBrickNames=("${subBrickNames[@]}" "$2") #append this suffix to the list of subBrickNames
    done

    #join sub-brick names with a | to allow for alternation checking by grep
    joinedNames=$(printf "\|%s" "${subBrickNames[@]}")

    #chop off the leading \|
    joinedNames=${joinedNames:2}

    #move the extracted coefficients to the output directory
    #grep -z to accept list separated by nulls and pass along to xargs with null (allows for spaces in filenames
    #xargs -0 to divide arguments by null character (passed via grep -z), -I to define "{}" as the passed-in list of files
    find ./ -type f -print0 | grep -z "${subject}_\(${joinedNames}\).*" | xargs -0 -I {} mv {} $outputDir

done