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Diffusion echo spacing units #291

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merged 3 commits into from
May 1, 2024
Merged

Diffusion echo spacing units #291

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338dab5
give outer diffusion script a seconds option for echo spacing
coalsont Apr 29, 2024
1e71908
Update DiffusionPreprocessing/DiffPreprocPipeline.sh
coalsont Apr 30, 2024
814e15c
update diffusion example to seconds
coalsont Apr 30, 2024
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35 changes: 33 additions & 2 deletions DiffusionPreprocessing/DiffPreprocPipeline.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -184,7 +184,8 @@ opts_AddMandatory '--posData' 'PosInputImages' 'data_RL1@data_RL2@...data_RLn' "

opts_AddMandatory '--negData' 'NegInputImages' 'data_LR1@data_LR2@...data_LRn' "An @ symbol separated list of data with 'negative' phase encoding direction; e.g., data_LR1@data_LR2@...data_LRn, or data_AP1@data_AP2@...data_APn"

opts_AddMandatory '--echospacing' 'echospacing' 'Number in msec' "Echo spacing in msecs"
opts_AddOptional '--echospacing-seconds' 'echospacingsec' 'Number in sec' "Echo spacing in seconds, REQUIRED (or deprecated millisec option)"
opts_AddOptional '--echospacing' 'echospacing' 'Number in millisec' "DEPRECATED: please use --echospacing-seconds"

opts_AddMandatory '--gdcoeffs' 'GdCoeffs' 'Path' "Path to file containing coefficients that describe spatial variations of the scanner gradients. Applied *after* 'eddy'. Use --gdcoeffs=NONE if not available."

Expand Down Expand Up @@ -248,6 +249,36 @@ then
TopupConfig="${HCPPIPEDIR_Config}/b02b0.cnf"
fi

#resolve echo spacing being required and exclusivity
if [[ "$echospacing" == "" && "$echospacingsec" == "" ]]
then
log_Err_Abort "You must specify --echospacing-seconds or --echospacing"
fi

if [[ "$echospacing" != "" && "$echospacingsec" != "" ]]
then
log_Err_Abort "You must not specify both --echospacing-seconds and --echospacing"
fi

#internally, PreEddy script expects milliseconds
if [[ "$echospacingsec" != "" ]]
then
echospacingmilli=$(echo "$echospacingsec * 1000" | bc -l)
else
#could add a deprecation warning here, if we want to remove the old parameter in the future
echospacingmilli="$echospacing"
fi

#check for input unit errors
if [[ $(echo "$echospacingmilli < 10 && $echospacingmilli > 0.01" | bc) == 0* ]]
then
log_Err_Abort "$echospacingmilli milliseconds is not a sane value for echo spacing"
fi
if [[ $(echo "$echospacingmilli < 1 && $echospacingmilli > 0.1" | bc) == 0* ]]
then
log_Warn "$echospacingmilli milliseconds seems unlikely for echo spacing, continuing anyway"
fi

"$HCPPIPEDIR"/show_version

# Verify required environment variables are set and log value
Expand Down Expand Up @@ -320,7 +351,7 @@ pre_eddy_cmd=("${HCPPIPEDIR}/DiffusionPreprocessing/DiffPreprocPipeline_PreEddy.
"--PEdir=${PEdir}"
"--posData=${PosInputImages}"
"--negData=${NegInputImages}"
"--echospacing=${echospacing}"
"--echospacing=${echospacingmilli}"
"--b0maxbval=${b0maxbval}"
"--topup-config-file=${TopupConfig}"
"--printcom=${runcmd}"
Expand Down
6 changes: 3 additions & 3 deletions Examples/Scripts/DiffusionPreprocessingBatch.sh
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Expand Up @@ -131,13 +131,13 @@ for Subject in $Subjlist ; do
PosData="${RawDataDir}/${SubjectID}_3T_DWI_dir95_RL.nii.gz@${RawDataDir}/${SubjectID}_3T_DWI_dir96_RL.nii.gz@${RawDataDir}/${SubjectID}_3T_DWI_dir97_RL.nii.gz"
NegData="${RawDataDir}/${SubjectID}_3T_DWI_dir95_LR.nii.gz@${RawDataDir}/${SubjectID}_3T_DWI_dir96_LR.nii.gz@${RawDataDir}/${SubjectID}_3T_DWI_dir97_LR.nii.gz"

# "Effective" Echo Spacing of dMRI image (specified in *msec* for the dMRI processing)
# "Effective" Echo Spacing of dMRI image (now specified in seconds for the dMRI processing)
# EchoSpacing = 1/(BWPPPE * ReconMatrixPE)
# where BWPPPE is the "BandwidthPerPixelPhaseEncode" = DICOM field (0019,1028) for Siemens, and
# ReconMatrixPE = size of the reconstructed image in the PE dimension
# In-plane acceleration, phase oversampling, phase resolution, phase field-of-view, and interpolation
# all potentially need to be accounted for (which they are in Siemen's reported BWPPPE)
EchoSpacing=0.78
EchoSpacingSec=0.00078

PEdir=1 #Use 1 for Left-Right Phase Encoding, 2 for Anterior-Posterior

Expand All @@ -158,7 +158,7 @@ for Subject in $Subjlist ; do
"${queuing_command[@]}" "${HCPPIPEDIR}"/DiffusionPreprocessing/DiffPreprocPipeline.sh \
--posData="${PosData}" --negData="${NegData}" \
--path="${StudyFolder}" --subject="${SubjectID}" \
--echospacing="${EchoSpacing}" --PEdir="${PEdir}" \
--echospacing-seconds="${EchoSpacingSec}" --PEdir="${PEdir}" \
--gdcoeffs="${Gdcoeffs}" \
--printcom="$PRINTCOM"

Expand Down