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Merge pull request #70 from Washington-University/feature/TaskfMRIAna…
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    add and clarify comments for better understanding by user
    move and consolidate commands into 'functional blocks' of code that perform the same function
    improve syntax of string comparisons in if statements
        quote all variables to avoid syntax error if variable is null
        consolidate multiple tests [ ! "$a" = "$b" ] into single test [ "$a" != "$b" ]
    modify output scalar names to include "zstat" and "cope"
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@glasserm
glasserm authored May 17, 2018
2 parents 56f10c0 + ae57352 commit 2b66fe9
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231 changes: 99 additions & 132 deletions TaskfMRIAnalysis/TaskfMRIAnalysis.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -41,42 +41,22 @@
# and does not attempt any further processing.
set -e

# Load function libraries
source ${HCPPIPEDIR}/global/scripts/log.shlib # Logging related functions
source ${HCPPIPEDIR}/global/scripts/opts.shlib # Command line option funtions

# Establish tool name for logging
log_SetToolName "TaskfMRIAnalysis.sh"

# Other utility functions

get_fsl_version()
{
local fsl_version_file
local fsl_version
local __functionResultVar=${1}
########################################## PREPARE FUNCTIONS ##########################################

fsl_version_file="${FSLDIR}/etc/fslversion"

if [ -f ${fsl_version_file} ]
then
fsl_version=`cat ${fsl_version_file}`
log_Msg "INFO: Determined that the FSL version in use is ${fsl_version}"
else
log_Msg "ERROR: Cannot tell which version of FSL you are using."
exit 1
fi
# Load function libraries
source ${HCPPIPEDIR}/global/scripts/log.shlib # Logging related functions
source ${HCPPIPEDIR}/global/scripts/opts.shlib # Command line option functions
source ${HCPPIPEDIR}/global/scripts/fsl_version.shlib # Function for getting FSL version

eval $__functionResultVar="'${fsl_version}'"
}

#
# NOTE:
# Don't echo anything in this function other than the last echo
# that outputs the return value
#
# function to test FSL versions
determine_old_or_new_fsl()
{
# NOTE:
# Don't echo anything in this function other than the last echo
# that outputs the return value
#
local fsl_version=${1}
local old_or_new
local fsl_version_array
Expand Down Expand Up @@ -130,135 +110,122 @@ determine_old_or_new_fsl()
}


########################################## READ_ARGS ##################################

# Explcitly set tool name for logging
log_SetToolName "TaskfMRIAnalysis.sh"

# Show version of HCP Pipeline Scripts in use if requested
opts_ShowVersionIfRequested $@

log_Msg "Parsing Command Line Options"

# Parse expected arguments from command-line array
log_Msg "READ_ARGS: Parsing Command Line Options"
Path=`opts_GetOpt1 "--path" $@`
log_Msg "Path: ${Path}"

Subject=`opts_GetOpt1 "--subject" $@`
log_Msg "Subject: ${Subject}"

LevelOnefMRINames=`opts_GetOpt1 "--lvl1tasks" $@`
log_Msg "LevelOnefMRINames: ${LevelOnefMRINames}"

LevelOnefsfNames=`opts_GetOpt1 "--lvl1fsfs" $@`
log_Msg "LevelOnefsfNames: ${LevelOnefsfNames}"

LevelTwofMRIName=`opts_GetOpt1 "--lvl2task" $@`
log_Msg "LevelTwofMRIName: ${LevelTwofMRIName}"

LevelTwofsfNames=`opts_GetOpt1 "--lvl2fsf" $@`
log_Msg "LevelTwofsfNames: ${LevelTwofsfNames}"

LowResMesh=`opts_GetOpt1 "--lowresmesh" $@`
log_Msg "LowResMesh: ${LowResMesh}"

GrayordinatesResolution=`opts_GetOpt1 "--grayordinatesres" $@`
log_Msg "GrayordinatesResolution: ${GrayordinatesResolution}"

OriginalSmoothingFWHM=`opts_GetOpt1 "--origsmoothingFWHM" $@`
log_Msg "OriginalSmoothingFWHM: ${OriginalSmoothingFWHM}"

Confound=`opts_GetOpt1 "--confound" $@`
log_Msg "Confound: ${Confound}"

FinalSmoothingFWHM=`opts_GetOpt1 "--finalsmoothingFWHM" $@`
log_Msg "FinalSmoothingFWHM: ${FinalSmoothingFWHM}"

TemporalFilter=`opts_GetOpt1 "--temporalfilter" $@`
log_Msg "TemporalFilter: ${TemporalFilter}"

VolumeBasedProcessing=`opts_GetOpt1 "--vba" $@`
log_Msg "VolumeBasedProcessing: ${VolumeBasedProcessing}"

RegName=`opts_GetOpt1 "--regname" $@`
log_Msg "RegName: ${RegName}"

Parcellation=`opts_GetOpt1 "--parcellation" $@`
log_Msg "Parcellation: ${Parcellation}"

ParcellationFile=`opts_GetOpt1 "--parcellationfile" $@`
log_Msg "ParcellationFile: ${ParcellationFile}"

# Determine the version of FSL that is in use
get_fsl_version fsl_ver
log_Msg "FSL version: ${fsl_ver}"

# Determine whether to invoke the "OLD" (v1.0) or "NEW" (v2.0) version of Task fMRI Analysis
# Write command-line arguments to log file
log_Msg "READ_ARGS: Path: ${Path}"
log_Msg "READ_ARGS: Subject: ${Subject}"
log_Msg "READ_ARGS: LevelOnefMRINames: ${LevelOnefMRINames}"
log_Msg "READ_ARGS: LevelOnefsfNames: ${LevelOnefsfNames}"
log_Msg "READ_ARGS: LevelTwofMRIName: ${LevelTwofMRIName}"
log_Msg "READ_ARGS: LevelTwofsfNames: ${LevelTwofsfNames}"
log_Msg "READ_ARGS: LowResMesh: ${LowResMesh}"
log_Msg "READ_ARGS: GrayordinatesResolution: ${GrayordinatesResolution}"
log_Msg "READ_ARGS: OriginalSmoothingFWHM: ${OriginalSmoothingFWHM}"
log_Msg "READ_ARGS: Confound: ${Confound}"
log_Msg "READ_ARGS: FinalSmoothingFWHM: ${FinalSmoothingFWHM}"
log_Msg "READ_ARGS: TemporalFilter: ${TemporalFilter}"
log_Msg "READ_ARGS: VolumeBasedProcessing: ${VolumeBasedProcessing}"
log_Msg "READ_ARGS: RegName: ${RegName}"
log_Msg "READ_ARGS: Parcellation: ${Parcellation}"
log_Msg "READ_ARGS: ParcellationFile: ${ParcellationFile}"


########################################## MAIN #########################################

# Determine if required FSL version is present
fsl_version_get fsl_ver
old_or_new_version=$(determine_old_or_new_fsl ${fsl_ver})

if [ "${old_or_new_version}" == "OLD" ]
then
# Need to exit script due to incompatible FSL VERSION!!!!
log_Msg "ERROR: Detected pre-5.0.7 version of FSL is in use. Task fMRI Analysis not invoked."
log_Msg "MAIN: TEST_FSL_VERSION: ERROR: Detected pre-5.0.7 version of FSL in use (version ${fsl_ver}). Task fMRI Analysis not invoked. Exiting."
exit 1
else
log_Msg "INFO: Detected version 5.0.7 or newer of FSL is in use. Invoking Level1 and Level2 scripts."

#Naming Conventions
AtlasFolder="${Path}/${Subject}/MNINonLinear"
ResultsFolder="${AtlasFolder}/Results"
ROIsFolder="${AtlasFolder}/ROIs"
DownSampleFolder="${AtlasFolder}/fsaverage_LR${LowResMesh}k"

#Run Level One Analysis for Both Phase Encoding Directions
log_Msg "Run Level One Analysis for Both Phase Encoding Directions"

LevelOnefMRINames=`echo $LevelOnefMRINames | sed 's/@/ /g'`
LevelOnefsfNames=`echo $LevelOnefsfNames | sed 's/@/ /g'`

i=1
for LevelOnefMRIName in $LevelOnefMRINames ; do
log_Msg "LevelOnefMRIName: ${LevelOnefMRIName}"
LevelOnefsfName=`echo $LevelOnefsfNames | cut -d " " -f $i`
log_Msg "Issued command: ${HCPPIPEDIR_tfMRIAnalysis}/TaskfMRILevel1.sh $Subject $ResultsFolder $ROIsFolder $DownSampleFolder $LevelOnefMRIName $LevelOnefsfName $LowResMesh $GrayordinatesResolution $OriginalSmoothingFWHM $Confound $FinalSmoothingFWHM $TemporalFilter $VolumeBasedProcessing $RegName $Parcellation $ParcellationFile"
${HCPPIPEDIR_tfMRIAnalysis}/TaskfMRILevel1.sh \
$Subject \
$ResultsFolder \
$ROIsFolder \
$DownSampleFolder \
$LevelOnefMRIName \
$LevelOnefsfName \
$LowResMesh \
$GrayordinatesResolution \
$OriginalSmoothingFWHM \
$Confound \
$FinalSmoothingFWHM \
$TemporalFilter \
$VolumeBasedProcessing \
$RegName \
$Parcellation \
$ParcellationFile
i=$(($i+1))
done

if [ "$LevelTwofMRIName" != "NONE" ]
then
LevelOnefMRINames=`echo $LevelOnefMRINames | sed 's/ /@/g'`
LevelOnefsfNames=`echo $LevelOnefMRINames | sed 's/ /@/g'`
log_Msg "MAIN: TEST_FSL_VERSION: Beginning analyses with FSL version ${fsl_ver}"
fi

#Combine Data Across Phase Encoding Directions in the Level Two Analysis
log_Msg "Combine Data Across Phase Encoding Directions in the Level Two Analysis"
log_Msg "Issued command: ${HCPPIPEDIR_tfMRIAnalysis}/TaskfMRILevel2.sh $Subject $ResultsFolder $DownSampleFolder $LevelOnefMRINames $LevelOnefsfNames $LevelTwofMRIName $LevelTwofsfNames $LowResMesh $FinalSmoothingFWHM $TemporalFilter $VolumeBasedProcessing $RegName $Parcellation"
${HCPPIPEDIR_tfMRIAnalysis}/TaskfMRILevel2.sh \
$Subject \
$ResultsFolder \
$DownSampleFolder \
$LevelOnefMRINames \
$LevelOnefsfNames \
$LevelTwofMRIName \
$LevelTwofsfNames \
$LowResMesh \
$FinalSmoothingFWHM \
$TemporalFilter \
$VolumeBasedProcessing \
$RegName \
$Parcellation
fi
# Determine locations of necessary directories (using expected naming convention)
AtlasFolder="${Path}/${Subject}/MNINonLinear"
ResultsFolder="${AtlasFolder}/Results"
ROIsFolder="${AtlasFolder}/ROIs"
DownSampleFolder="${AtlasFolder}/fsaverage_LR${LowResMesh}k"


# Run Level 1 analyses for each phase encoding direction (from command line arguments)
log_Msg "MAIN: RUN_LEVEL1: Running Level 1 Analysis for Both Phase Encoding Directions"
i=1
# Level 1 analysis names were delimited by '@' in command-line; change to space in for loop
for LevelOnefMRIName in $( echo $LevelOnefMRINames | sed 's/@/ /g' ) ; do
log_Msg "MAIN: RUN_LEVEL1: LevelOnefMRIName: ${LevelOnefMRIName}"
# Get corresponding fsf name from $LevelOnefsfNames list
LevelOnefsfName=`echo $LevelOnefsfNames | cut -d "@" -f $i`
log_Msg "MAIN: RUN_LEVEL1: Issuing command: ${HCPPIPEDIR_tfMRIAnalysis}/TaskfMRILevel1.sh $Subject $ResultsFolder $ROIsFolder $DownSampleFolder $LevelOnefMRIName $LevelOnefsfName $LowResMesh $GrayordinatesResolution $OriginalSmoothingFWHM $Confound $FinalSmoothingFWHM $TemporalFilter $VolumeBasedProcessing $RegName $Parcellation $ParcellationFile"
${HCPPIPEDIR_tfMRIAnalysis}/TaskfMRILevel1.sh \
$Subject \
$ResultsFolder \
$ROIsFolder \
$DownSampleFolder \
$LevelOnefMRIName \
$LevelOnefsfName \
$LowResMesh \
$GrayordinatesResolution \
$OriginalSmoothingFWHM \
$Confound \
$FinalSmoothingFWHM \
$TemporalFilter \
$VolumeBasedProcessing \
$RegName \
$Parcellation \
$ParcellationFile
i=$(($i+1))
done

if [ "$LevelTwofMRIName" != "NONE" ]
then
# Combine Data Across Phase Encoding Directions in the Level 2 Analysis
log_Msg "MAIN: RUN_LEVEL2: Combine Data Across Phase Encoding Directions in the Level 2 Analysis"
log_Msg "MAIN: RUN_LEVEL2: Issuing command: ${HCPPIPEDIR_tfMRIAnalysis}/TaskfMRILevel2.sh $Subject $ResultsFolder $DownSampleFolder $LevelOnefMRINames $LevelOnefsfNames $LevelTwofMRIName $LevelTwofsfNames $LowResMesh $FinalSmoothingFWHM $TemporalFilter $VolumeBasedProcessing $RegName $Parcellation"
${HCPPIPEDIR_tfMRIAnalysis}/TaskfMRILevel2.sh \
$Subject \
$ResultsFolder \
$DownSampleFolder \
$LevelOnefMRINames \
$LevelOnefsfNames \
$LevelTwofMRIName \
$LevelTwofsfNames \
$LowResMesh \
$FinalSmoothingFWHM \
$TemporalFilter \
$VolumeBasedProcessing \
$RegName \
$Parcellation
fi

log_Msg "Completed"
log_Msg "MAIN: Completed"

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