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Transmit bias pipeline #298

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merged 11 commits into from
Nov 15, 2024
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fix bugs in RunIndividual and interpreted matlab, change RunIndividua…
…l default to compiled
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coalsont committed Oct 29, 2024
commit 5bed47c711ebb0485581bf5fff1ff06eea584da1
15 changes: 4 additions & 11 deletions TransmitBias/RunIndividualOnly.sh
Original file line number Diff line number Diff line change
@@ -64,10 +64,10 @@ opts_AddOptional '--grayordinates-res' 'grayordRes' 'number' "resolution used in
opts_AddOptional '--transmit-res' 'transmitRes' 'number' "resolution to use for transmit field, default equal to --grayordinates-res"
opts_AddOptional '--myelin-mapping-fwhm' 'MyelinMappingFWHM' 'number' "fwhm value to use in -myelin-style, default 5" '5'
opts_AddOptional '--old-myelin-mapping' 'oldmappingStr' 'TRUE or FALSE' "if myelin mapping was done using version 1.2.3 or earlier of wb_command, set this to true" 'false'
opts_AddOptional '--matlab-run-mode' 'MatlabMode' '0, 1, or 2' "defaults to 1
opts_AddOptional '--matlab-run-mode' 'MatlabMode' '0, 1, or 2' "defaults to 0
0 = compiled MATLAB
1 = interpreted MATLAB
2 = Octave" '1'
2 = Octave" '0'

opts_ParseArguments "$@"

@@ -86,14 +86,7 @@ then
fi

case "$MatlabMode" in
(0)
if [[ "${MATLAB_COMPILER_RUNTIME:-}" == "" ]]
then
log_Err_Abort "To use compiled matlab, you must set and export the variable MATLAB_COMPILER_RUNTIME"
fi
log_Err_Abort "compiled matlab not implemented"
;;
(1|2)
(0|1|2)
;;
(*)
log_Err_Abort "unrecognized matlab mode '$MatlabMode', use 0, 1, or 2"
@@ -115,7 +108,7 @@ case "$mode" in
fi
;;
(PseudoTransmit)
if [[ "$fMRINames" == "" || "$ReferenceTemplate" == "" || "$GroupUncorrectedMyelin" == "" || "$PseudoTransmitReferenceValue" == "" ]]
if [[ "$fMRINames" == "" || "$ReferenceTemplate" == "" || "$GroupUncorrectedMyelin" == "" || "$PseudoTransmitReferenceValueFile" == "" ]]
then
log_Err_Abort "$mode transmit correction mode requires --pt-fmri-names, --myelin-template, --group-uncorrected-myelin, and --pt-reference-value"
fi
2 changes: 1 addition & 1 deletion TransmitBias/scripts/AFI_GroupAverage.sh
Original file line number Diff line number Diff line change
@@ -181,7 +181,7 @@ case "$MatlabMode" in
"

if [[ "$matlabargs" != "" ]]; then matlabargs+=", "; fi
matlabargs+="'$var'"
matlabargs+="$var"
done

matlabcode+="AFI_GroupAverage(${matlabargs});"
2 changes: 1 addition & 1 deletion TransmitBias/scripts/AFI_GroupAverageCorrectedMaps.sh
Original file line number Diff line number Diff line change
@@ -192,7 +192,7 @@ case "$MatlabMode" in
"

if [[ "$matlabargs" != "" ]]; then matlabargs+=", "; fi
matlabargs+="'$var'"
matlabargs+="$var"
done

matlabcode+="AFI_GroupAverageCorrectedMaps(${matlabargs});"
2 changes: 1 addition & 1 deletion TransmitBias/scripts/AFI_IndividualFitCorrection.sh
Original file line number Diff line number Diff line change
@@ -131,7 +131,7 @@ case "$MatlabMode" in
"

if [[ "$matlabargs" != "" ]]; then matlabargs+=", "; fi
matlabargs+="'$var'"
matlabargs+="$var"
done

matlabcode+="AFI_OptimizeSmoothing(${matlabargs});"
2 changes: 1 addition & 1 deletion TransmitBias/scripts/B1Tx_GroupAverage.sh
Original file line number Diff line number Diff line change
@@ -163,7 +163,7 @@ case "$MatlabMode" in
"

if [[ "$matlabargs" != "" ]]; then matlabargs+=", "; fi
matlabargs+="'$var'"
matlabargs+="$var"
done

matlabcode+="B1Tx_GroupAverage(${matlabargs});"
2 changes: 1 addition & 1 deletion TransmitBias/scripts/B1Tx_GroupAverageCorrectedMaps.sh
Original file line number Diff line number Diff line change
@@ -169,7 +169,7 @@ case "$MatlabMode" in
"

if [[ "$matlabargs" != "" ]]; then matlabargs+=", "; fi
matlabargs+="'$var'"
matlabargs+="$var"
done

matlabcode+="B1Tx_GroupAverageCorrectedMaps(${matlabargs});"
2 changes: 1 addition & 1 deletion TransmitBias/scripts/B1Tx_IndividualFitCorrection.sh
Original file line number Diff line number Diff line change
@@ -127,7 +127,7 @@ case "$MatlabMode" in
"

if [[ "$matlabargs" != "" ]]; then matlabargs+=", "; fi
matlabargs+="'$var'"
matlabargs+="$var"
done

matlabcode+="B1Tx_OptimizeSmoothing(${matlabargs});"
2 changes: 1 addition & 1 deletion TransmitBias/scripts/PseudoTransmit_GroupAverage.sh
Original file line number Diff line number Diff line change
@@ -146,7 +146,7 @@ case "$MatlabMode" in
"

if [[ "$matlabargs" != "" ]]; then matlabargs+=", "; fi
matlabargs+="'$var'"
matlabargs+="$var"
done

matlabcode+="PseudoTransmit_GroupAverage(${matlabargs});"
Original file line number Diff line number Diff line change
@@ -166,7 +166,7 @@ case "$MatlabMode" in
"

if [[ "$matlabargs" != "" ]]; then matlabargs+=", "; fi
matlabargs+="'$var'"
matlabargs+="$var"
done

matlabcode+="PseudoTransmit_GroupAverageCorrectedMaps(${matlabargs});"
Original file line number Diff line number Diff line change
@@ -141,7 +141,7 @@ case "$MatlabMode" in
"

if [[ "$matlabargs" != "" ]]; then matlabargs+=", "; fi
matlabargs+="'$var'"
matlabargs+="$var"
done

matlabcode+="PseudoTransmit_OptimizeSmoothing(${matlabargs});"