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Merge pull request #70 from Washington-University/feature/TaskfMRIAnalysis_combine_comment
 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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‎TaskfMRIAnalysis/TaskfMRIAnalysis.sh

Lines changed: 99 additions & 132 deletions
Original file line numberDiff line numberDiff line change
@@ -41,42 +41,22 @@
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# and does not attempt any further processing.
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set -e
4343

44-
# Load function libraries
45-
source ${HCPPIPEDIR}/global/scripts/log.shlib # Logging related functions
46-
source ${HCPPIPEDIR}/global/scripts/opts.shlib # Command line option funtions
47-
48-
# Establish tool name for logging
49-
log_SetToolName "TaskfMRIAnalysis.sh"
50-
51-
# Other utility functions
5244

53-
get_fsl_version()
54-
{
55-
local fsl_version_file
56-
local fsl_version
57-
local __functionResultVar=${1}
45+
########################################## PREPARE FUNCTIONS ##########################################
5846

59-
fsl_version_file="${FSLDIR}/etc/fslversion"
60-
61-
if [ -f ${fsl_version_file} ]
62-
then
63-
fsl_version=`cat ${fsl_version_file}`
64-
log_Msg "INFO: Determined that the FSL version in use is ${fsl_version}"
65-
else
66-
log_Msg "ERROR: Cannot tell which version of FSL you are using."
67-
exit 1
68-
fi
47+
# Load function libraries
48+
source ${HCPPIPEDIR}/global/scripts/log.shlib # Logging related functions
49+
source ${HCPPIPEDIR}/global/scripts/opts.shlib # Command line option functions
50+
source ${HCPPIPEDIR}/global/scripts/fsl_version.shlib # Function for getting FSL version
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70-
eval $__functionResultVar="'${fsl_version}'"
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}
7252

73-
#
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# NOTE:
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# Don't echo anything in this function other than the last echo
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# that outputs the return value
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#
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# function to test FSL versions
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determine_old_or_new_fsl()
7955
{
56+
# NOTE:
57+
# Don't echo anything in this function other than the last echo
58+
# that outputs the return value
59+
#
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local fsl_version=${1}
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local old_or_new
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local fsl_version_array
@@ -130,135 +110,122 @@ determine_old_or_new_fsl()
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}
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132112

113+
########################################## READ_ARGS ##################################
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115+
# Explcitly set tool name for logging
116+
log_SetToolName "TaskfMRIAnalysis.sh"
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133118
# Show version of HCP Pipeline Scripts in use if requested
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opts_ShowVersionIfRequested $@
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136-
log_Msg "Parsing Command Line Options"
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121+
# Parse expected arguments from command-line array
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log_Msg "READ_ARGS: Parsing Command Line Options"
138123
Path=`opts_GetOpt1 "--path" $@`
139-
log_Msg "Path: ${Path}"
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141124
Subject=`opts_GetOpt1 "--subject" $@`
142-
log_Msg "Subject: ${Subject}"
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144125
LevelOnefMRINames=`opts_GetOpt1 "--lvl1tasks" $@`
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log_Msg "LevelOnefMRINames: ${LevelOnefMRINames}"
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LevelOnefsfNames=`opts_GetOpt1 "--lvl1fsfs" $@`
148-
log_Msg "LevelOnefsfNames: ${LevelOnefsfNames}"
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150127
LevelTwofMRIName=`opts_GetOpt1 "--lvl2task" $@`
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log_Msg "LevelTwofMRIName: ${LevelTwofMRIName}"
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153128
LevelTwofsfNames=`opts_GetOpt1 "--lvl2fsf" $@`
154-
log_Msg "LevelTwofsfNames: ${LevelTwofsfNames}"
155-
156129
LowResMesh=`opts_GetOpt1 "--lowresmesh" $@`
157-
log_Msg "LowResMesh: ${LowResMesh}"
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GrayordinatesResolution=`opts_GetOpt1 "--grayordinatesres" $@`
160-
log_Msg "GrayordinatesResolution: ${GrayordinatesResolution}"
161-
162131
OriginalSmoothingFWHM=`opts_GetOpt1 "--origsmoothingFWHM" $@`
163-
log_Msg "OriginalSmoothingFWHM: ${OriginalSmoothingFWHM}"
164-
165132
Confound=`opts_GetOpt1 "--confound" $@`
166-
log_Msg "Confound: ${Confound}"
167-
168133
FinalSmoothingFWHM=`opts_GetOpt1 "--finalsmoothingFWHM" $@`
169-
log_Msg "FinalSmoothingFWHM: ${FinalSmoothingFWHM}"
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171134
TemporalFilter=`opts_GetOpt1 "--temporalfilter" $@`
172-
log_Msg "TemporalFilter: ${TemporalFilter}"
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174135
VolumeBasedProcessing=`opts_GetOpt1 "--vba" $@`
175-
log_Msg "VolumeBasedProcessing: ${VolumeBasedProcessing}"
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177136
RegName=`opts_GetOpt1 "--regname" $@`
178-
log_Msg "RegName: ${RegName}"
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180137
Parcellation=`opts_GetOpt1 "--parcellation" $@`
181-
log_Msg "Parcellation: ${Parcellation}"
182-
183138
ParcellationFile=`opts_GetOpt1 "--parcellationfile" $@`
184-
log_Msg "ParcellationFile: ${ParcellationFile}"
185139

186-
# Determine the version of FSL that is in use
187-
get_fsl_version fsl_ver
188-
log_Msg "FSL version: ${fsl_ver}"
189-
190-
# Determine whether to invoke the "OLD" (v1.0) or "NEW" (v2.0) version of Task fMRI Analysis
140+
# Write command-line arguments to log file
141+
log_Msg "READ_ARGS: Path: ${Path}"
142+
log_Msg "READ_ARGS: Subject: ${Subject}"
143+
log_Msg "READ_ARGS: LevelOnefMRINames: ${LevelOnefMRINames}"
144+
log_Msg "READ_ARGS: LevelOnefsfNames: ${LevelOnefsfNames}"
145+
log_Msg "READ_ARGS: LevelTwofMRIName: ${LevelTwofMRIName}"
146+
log_Msg "READ_ARGS: LevelTwofsfNames: ${LevelTwofsfNames}"
147+
log_Msg "READ_ARGS: LowResMesh: ${LowResMesh}"
148+
log_Msg "READ_ARGS: GrayordinatesResolution: ${GrayordinatesResolution}"
149+
log_Msg "READ_ARGS: OriginalSmoothingFWHM: ${OriginalSmoothingFWHM}"
150+
log_Msg "READ_ARGS: Confound: ${Confound}"
151+
log_Msg "READ_ARGS: FinalSmoothingFWHM: ${FinalSmoothingFWHM}"
152+
log_Msg "READ_ARGS: TemporalFilter: ${TemporalFilter}"
153+
log_Msg "READ_ARGS: VolumeBasedProcessing: ${VolumeBasedProcessing}"
154+
log_Msg "READ_ARGS: RegName: ${RegName}"
155+
log_Msg "READ_ARGS: Parcellation: ${Parcellation}"
156+
log_Msg "READ_ARGS: ParcellationFile: ${ParcellationFile}"
157+
158+
159+
########################################## MAIN #########################################
160+
161+
# Determine if required FSL version is present
162+
fsl_version_get fsl_ver
191163
old_or_new_version=$(determine_old_or_new_fsl ${fsl_ver})
192-
193164
if [ "${old_or_new_version}" == "OLD" ]
194165
then
195166
# Need to exit script due to incompatible FSL VERSION!!!!
196-
log_Msg "ERROR: Detected pre-5.0.7 version of FSL is in use. Task fMRI Analysis not invoked."
167+
log_Msg "MAIN: TEST_FSL_VERSION: ERROR: Detected pre-5.0.7 version of FSL in use (version ${fsl_ver}). Task fMRI Analysis not invoked. Exiting."
197168
exit 1
198169
else
199-
log_Msg "INFO: Detected version 5.0.7 or newer of FSL is in use. Invoking Level1 and Level2 scripts."
200-
201-
#Naming Conventions
202-
AtlasFolder="${Path}/${Subject}/MNINonLinear"
203-
ResultsFolder="${AtlasFolder}/Results"
204-
ROIsFolder="${AtlasFolder}/ROIs"
205-
DownSampleFolder="${AtlasFolder}/fsaverage_LR${LowResMesh}k"
206-
207-
#Run Level One Analysis for Both Phase Encoding Directions
208-
log_Msg "Run Level One Analysis for Both Phase Encoding Directions"
209-
210-
LevelOnefMRINames=`echo $LevelOnefMRINames | sed 's/@/ /g'`
211-
LevelOnefsfNames=`echo $LevelOnefsfNames | sed 's/@/ /g'`
212-
213-
i=1
214-
for LevelOnefMRIName in $LevelOnefMRINames ; do
215-
log_Msg "LevelOnefMRIName: ${LevelOnefMRIName}"
216-
LevelOnefsfName=`echo $LevelOnefsfNames | cut -d " " -f $i`
217-
log_Msg "Issued command: ${HCPPIPEDIR_tfMRIAnalysis}/TaskfMRILevel1.sh $Subject $ResultsFolder $ROIsFolder $DownSampleFolder $LevelOnefMRIName $LevelOnefsfName $LowResMesh $GrayordinatesResolution $OriginalSmoothingFWHM $Confound $FinalSmoothingFWHM $TemporalFilter $VolumeBasedProcessing $RegName $Parcellation $ParcellationFile"
218-
${HCPPIPEDIR_tfMRIAnalysis}/TaskfMRILevel1.sh \
219-
$Subject \
220-
$ResultsFolder \
221-
$ROIsFolder \
222-
$DownSampleFolder \
223-
$LevelOnefMRIName \
224-
$LevelOnefsfName \
225-
$LowResMesh \
226-
$GrayordinatesResolution \
227-
$OriginalSmoothingFWHM \
228-
$Confound \
229-
$FinalSmoothingFWHM \
230-
$TemporalFilter \
231-
$VolumeBasedProcessing \
232-
$RegName \
233-
$Parcellation \
234-
$ParcellationFile
235-
i=$(($i+1))
236-
done
237-
238-
if [ "$LevelTwofMRIName" != "NONE" ]
239-
then
240-
LevelOnefMRINames=`echo $LevelOnefMRINames | sed 's/ /@/g'`
241-
LevelOnefsfNames=`echo $LevelOnefMRINames | sed 's/ /@/g'`
170+
log_Msg "MAIN: TEST_FSL_VERSION: Beginning analyses with FSL version ${fsl_ver}"
171+
fi
242172

243-
#Combine Data Across Phase Encoding Directions in the Level Two Analysis
244-
log_Msg "Combine Data Across Phase Encoding Directions in the Level Two Analysis"
245-
log_Msg "Issued command: ${HCPPIPEDIR_tfMRIAnalysis}/TaskfMRILevel2.sh $Subject $ResultsFolder $DownSampleFolder $LevelOnefMRINames $LevelOnefsfNames $LevelTwofMRIName $LevelTwofsfNames $LowResMesh $FinalSmoothingFWHM $TemporalFilter $VolumeBasedProcessing $RegName $Parcellation"
246-
${HCPPIPEDIR_tfMRIAnalysis}/TaskfMRILevel2.sh \
247-
$Subject \
248-
$ResultsFolder \
249-
$DownSampleFolder \
250-
$LevelOnefMRINames \
251-
$LevelOnefsfNames \
252-
$LevelTwofMRIName \
253-
$LevelTwofsfNames \
254-
$LowResMesh \
255-
$FinalSmoothingFWHM \
256-
$TemporalFilter \
257-
$VolumeBasedProcessing \
258-
$RegName \
259-
$Parcellation
260-
fi
173+
# Determine locations of necessary directories (using expected naming convention)
174+
AtlasFolder="${Path}/${Subject}/MNINonLinear"
175+
ResultsFolder="${AtlasFolder}/Results"
176+
ROIsFolder="${AtlasFolder}/ROIs"
177+
DownSampleFolder="${AtlasFolder}/fsaverage_LR${LowResMesh}k"
178+
179+
180+
# Run Level 1 analyses for each phase encoding direction (from command line arguments)
181+
log_Msg "MAIN: RUN_LEVEL1: Running Level 1 Analysis for Both Phase Encoding Directions"
182+
i=1
183+
# Level 1 analysis names were delimited by '@' in command-line; change to space in for loop
184+
for LevelOnefMRIName in $( echo $LevelOnefMRINames | sed 's/@/ /g' ) ; do
185+
log_Msg "MAIN: RUN_LEVEL1: LevelOnefMRIName: ${LevelOnefMRIName}"
186+
# Get corresponding fsf name from $LevelOnefsfNames list
187+
LevelOnefsfName=`echo $LevelOnefsfNames | cut -d "@" -f $i`
188+
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"
189+
${HCPPIPEDIR_tfMRIAnalysis}/TaskfMRILevel1.sh \
190+
$Subject \
191+
$ResultsFolder \
192+
$ROIsFolder \
193+
$DownSampleFolder \
194+
$LevelOnefMRIName \
195+
$LevelOnefsfName \
196+
$LowResMesh \
197+
$GrayordinatesResolution \
198+
$OriginalSmoothingFWHM \
199+
$Confound \
200+
$FinalSmoothingFWHM \
201+
$TemporalFilter \
202+
$VolumeBasedProcessing \
203+
$RegName \
204+
$Parcellation \
205+
$ParcellationFile
206+
i=$(($i+1))
207+
done
208+
209+
if [ "$LevelTwofMRIName" != "NONE" ]
210+
then
211+
# Combine Data Across Phase Encoding Directions in the Level 2 Analysis
212+
log_Msg "MAIN: RUN_LEVEL2: Combine Data Across Phase Encoding Directions in the Level 2 Analysis"
213+
log_Msg "MAIN: RUN_LEVEL2: Issuing command: ${HCPPIPEDIR_tfMRIAnalysis}/TaskfMRILevel2.sh $Subject $ResultsFolder $DownSampleFolder $LevelOnefMRINames $LevelOnefsfNames $LevelTwofMRIName $LevelTwofsfNames $LowResMesh $FinalSmoothingFWHM $TemporalFilter $VolumeBasedProcessing $RegName $Parcellation"
214+
${HCPPIPEDIR_tfMRIAnalysis}/TaskfMRILevel2.sh \
215+
$Subject \
216+
$ResultsFolder \
217+
$DownSampleFolder \
218+
$LevelOnefMRINames \
219+
$LevelOnefsfNames \
220+
$LevelTwofMRIName \
221+
$LevelTwofsfNames \
222+
$LowResMesh \
223+
$FinalSmoothingFWHM \
224+
$TemporalFilter \
225+
$VolumeBasedProcessing \
226+
$RegName \
227+
$Parcellation
261228
fi
262229

263-
log_Msg "Completed"
230+
log_Msg "MAIN: Completed"
264231

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