No more slice removal for odd number of slices

DiffusionPreprocessing/DiffPreprocPipeline.sh

@@ -134,17 +134,22 @@ PARAMETERs are: [ ] = optional; < > = user supplied value
   [--b0maxbval=<b0-max-bval>]
                           Volumes with a bvalue smaller than this value will be
                           considered as b0s. Defaults to ${DEFAULT_B0_MAX_BVAL}
-  [--printcom=<print-command>]
-                          Use the specified <print-command> to echo or otherwise
-                          output the commands that would be executed instead of
-                          actually running them. --printcom=echo is intended to
-                          be used for testing purposes
+  [--topup-config-file=<filename>]
+                          File containing the FSL topup configuration.
+                          Defaults to b02b0.cnf in the HCP configuration
+                          directory (as defined by ${HCPPIPEDIR_Config}).
   [--select-best-b0]
                           If set selects the best b0 for each phase encoding direction
                           to pass on to topup rather than the default behaviour of
                           using equally spaced b0's throughout the scan. The best b0
                           is identified as the least distorted (i.e., most similar to
                           the average b0 after registration).
+  [--ensure-even-slices]
+                          If set will ensure the input images to FSL's topup and eddy
+                          have an even number of slices by removing one slice if necessary.
+                          This behaviour used to be the default, but is now optional,
+                          because discarding a slice is incompatible with using slice-to-volume correction
+                          in FSL's eddy.
   [--extra-eddy-arg=<value>]
                           Generic single token (no whitespace) argument to pass
                           to the DiffPreprocPipeline_Eddy.sh script and subsequently
@@ -181,7 +186,6 @@ PARAMETERs are: [ ] = optional; < > = user supplied value
                           option can be used to specify which eddy_cuda binary
                           version to use. If specified, FSLDIR/bin/eddy_cudaX.Y
                           will be used.
-
   [--combine-data-flag=<value>]
                           Specified value is passed as the CombineDataFlag value
                           for the eddy_postproc.sh script.
@@ -194,6 +198,11 @@ PARAMETERs are: [ ] = optional; < > = user supplied value
                               acquired
                           0 - As 1, but also include uncombined single volumes
                           Defaults to 1
+  [--printcom=<print-command>]
+                          Use the specified <print-command> to echo or otherwise
+                          output the commands that would be executed instead of
+                          actually running them. --printcom=echo is intended to
+                          be used for testing purposes
 
 Return Status Value:
 
@@ -233,6 +242,7 @@ EOF
 #                         structural images
 #  ${b0maxbval}           Volumes with a bvalue smaller than this value will
 #                         be considered as b0s
+#  ${TopupConfig}         Filename with topup configuration
 #  ${runcmd}              Set to a user specifed command to use if user has
 #                         requested that commands be echo'd (or printed)
 #                         instead of actually executed. Otherwise, set to
@@ -269,9 +279,11 @@ get_options() {
 	DWIName="Diffusion"
 	DegreesOfFreedom=${DEFAULT_DEGREES_OF_FREEDOM}
 	b0maxbval=${DEFAULT_B0_MAX_BVAL}
+	TopupConfig=${HCPPIPEDIR_Config}/b02b0.cnf
 	runcmd=""
 	extra_eddy_args=""
 	SelectBestB0="false"
+	EnsureEvenSlices="false"
 	no_gpu="false"
 	cuda_version=""
 	CombineDataFlag=1
@@ -341,6 +353,14 @@ get_options() {
 			SelectBestB0="true"
 			index=$((index + 1))
 			;;
+		--ensure-even-slices)
+			EnsureEvenSlices="true"
+			index=$((index + 1))
+			;;
+		--topup-config-file=*)
+			TopupConfig=${argument#*=}
+			index=$((index + 1))
+			;;
 		--extra-eddy-arg=*)
 			extra_eddy_arg=${argument#*=}
 			extra_eddy_args+=" ${extra_eddy_arg} "
@@ -430,7 +450,9 @@ get_options() {
 	echo "   b0maxbval: ${b0maxbval}"
 	echo "   runcmd: ${runcmd}"
 	echo "   CombineDataFlag: ${CombineDataFlag}"
+	echo "   TopupConfig: ${TopupConfig}"
 	echo "   SelectBestB0: ${SelectBestB0}"
+	echo "   EnsureEvenSlices: ${EnsureEvenSlices}"
 	echo "   extra_eddy_args: ${extra_eddy_args}"
 	echo "   no_gpu: ${no_gpu}"
 	echo "   cuda-version: ${cuda_version}"
@@ -511,10 +533,14 @@ main() {
 	pre_eddy_cmd+=" --negData=${NegInputImages} "
 	pre_eddy_cmd+=" --echospacing=${echospacing} "
 	pre_eddy_cmd+=" --b0maxbval=${b0maxbval} "
+	pre_eddy_cmd+=" --topup-config-file=${TopupConfig} "
 	pre_eddy_cmd+=" --printcom=${runcmd} "
 	if [ "${SelectBestB0}" == "true" ]; then
 		pre_eddy_cmd+=" --select-best-b0 "
 	fi
+	if [ "${EnsureEvenSlices}" == "true" ]; then
+		pre_eddy_cmd+=" --ensure-even-slices "
+	fi
 
 	log_Msg "pre_eddy_cmd: ${pre_eddy_cmd}"
 	${pre_eddy_cmd}

DiffusionPreprocessing/DiffPreprocPipeline_Eddy.sh

@@ -119,11 +119,6 @@ PARAMETERs are: [ ] = optional; < > = user supplied value
   --subject=<subject-id>  subject ID
   [--dwiname=<DWIName>]   name to give DWI output directories
                           Defaults to Diffusion
-  [--printcom=<print-command>]
-                          Use the specified <print-command> to echo or otherwise
-                          output the commands that would be executed instead of
-                          actually running them. --printcom=echo is intended to
-                          be used for testing purposes
   [--dont_peas]           pass the --dont_peas (Do NOT perform a post-eddy
                           alignment of shells) option to the eddy invocation
   [--fwhm=<value>]        --fwhm value to pass to the eddy binary
@@ -149,6 +144,11 @@ PARAMETERs are: [ ] = optional; < > = user supplied value
                           option can be used to specify which eddy_cuda binary
                           version to use. If specified, FSLDIR/bin/eddy_cudaX.Y
                           will be used.
+  [--printcom=<print-command>]
+                          Use the specified <print-command> to echo or otherwise
+                          output the commands that would be executed instead of
+                          actually running them. --printcom=echo is intended to
+                          be used for testing purposes
 
 Return Status Value:
 

DiffusionPreprocessing/DiffPreprocPipeline_PostEddy.sh

@@ -88,11 +88,6 @@ PARAMETERs are: [ ] = optional; < > = user supplied value
   [--dof=<Degrees of Freedom>]
                           Degrees of Freedom for registration to structural
                           images. Defaults to ${DEFAULT_DEGREES_OF_FREEDOM}
-  [--printcom=<print-command>]
-                          Use the specified <print-command> to echo or otherwise
-                          output the commands that would be executed instead of
-                          actually running them. --printcom=echo is intended to
-                          be used for testing purposes
   [--select_best_b0]
                           Whether the --select-best-b0 flag was used in
                           DiffPreprocPipeline_PreEddy.
@@ -108,6 +103,11 @@ PARAMETERs are: [ ] = optional; < > = user supplied value
                               acquired
                           0 - As 1, but also include uncombined single volumes
                           Defaults to 1
+  [--printcom=<print-command>]
+                          Use the specified <print-command> to echo or otherwise
+                          output the commands that would be executed instead of
+                          actually running them. --printcom=echo is intended to
+                          be used for testing purposes
 
 Return Status Value:
 

DiffusionPreprocessing/DiffPreprocPipeline_PreEddy.sh

@@ -92,6 +92,8 @@ PARAMETERs are: [ ] = optional; < > = user supplied value
                             data_AP1@data_AP2@...data_APn
   --echospacing=<echo-spacing>
                           Effective Echo Spacing in msecs
+  --topup-config-file=<filename>
+                          File containing the FSL topup configuration.
   [--dwiname=<DWIname>]   name to give DWI output directories.
                           Defaults to Diffusion
   [--b0maxbval=<b0-max-bval>]
@@ -103,6 +105,12 @@ PARAMETERs are: [ ] = optional; < > = user supplied value
                           using equally spaced b0's throughout the scan. The best b0
                           is identified as the least distorted (i.e., most similar to
                           the average b0 after registration).
+  [--ensure-even-slices]
+                          If set will ensure the input images to FSL's topup and eddy
+                          have an even number of slices by removing one slice if necessary.
+                          This behaviour used to be the default, but is now optional,
+                          because discarding a slice is incompatible with using slice-to-volume correction
+                          in FSL's eddy.
   [--printcom=<print-command>]
                           Use the specified <print-command> to echo or otherwise
                           output the commands that would be executed instead of
@@ -138,8 +146,12 @@ EOF
 #                         encoding direction
 #  ${echospacing}         Echo spacing in msecs
 #  ${DWIName}             Name to give DWI output directories
+#  ${TopupConfig}         Filename with topup configuration
 #  ${b0maxbval}           Volumes with a bvalue smaller than this value will
 #                         be considered as b0s
+#  ${SelectBestB0}        If "true" will select the least distorted B0 for topup
+#  ${EnsureEvenSlices}    If "true" will ensure input images to topup/eddy have
+#                         even number of slices
 #  ${runcmd}              Set to a user specified command to use if user has
 #                         requested that commands be echo'd (or printed)
 #                         instead of actually executed. Otherwise, set to
@@ -150,6 +162,10 @@ EOF
 #  Support Functions
 # --------------------------------------------------------------------------------
 
+isodd() {
+	echo "$(($1 % 2))"
+}
+
 get_options() {
 	local arguments=($@)
 
@@ -161,10 +177,12 @@ get_options() {
 	unset NegInputImages
 	unset echospacing
 	unset SelectBestB0
+	unset TopupConfig
 	DWIName="Diffusion"
 	b0maxbval=${DEFAULT_B0_MAX_BVAL}
 	runcmd=""
 	SelectBestB0="false"
+	EnsureEvenSlices="false"
 
 	# parse arguments
 	local index=0
@@ -215,6 +233,10 @@ get_options() {
 			b0maxbval=${argument#*=}
 			index=$((index + 1))
 			;;
+		--topup-config-file=*)
+			TopupConfig=${argument#*=}
+			index=$((index + 1))
+			;;
 		--printcom=*)
 			runcmd=${argument#*=}
 			index=$((index + 1))
@@ -223,6 +245,10 @@ get_options() {
 			SelectBestB0="true"
 			index=$((index + 1))
 			;;
+		--ensure-even-slices)
+			EnsureEvenSlices="true"
+			index=$((index + 1))
+			;;
 		*)
 			show_usage
 			echo "ERROR: Unrecognized Option: ${argument}"
@@ -266,6 +292,10 @@ get_options() {
 		error_msgs+="\nERROR: <DWIName> not specified"
 	fi
 
+	if [ -z ${TopupConfig} ]; then
+		error_msgs+="\nERROR: <TopupConfig> not specified"
+	fi
+
 	if [ ! -z "${error_msgs}" ]; then
 		show_usage
 		echo -e ${error_msgs}
@@ -444,6 +474,18 @@ main() {
 		exit 1
 	fi
 
+	# if the number of slices are odd, check that the user has a way to deal with that
+	if [ "${EnsureEvenSlices}" == "false" ] && [ "${TopupConfig}" == "${HCPPIPEDIR_Config}/b02b0.cnf" ] ; then
+		dimz=$(${FSLDIR}/bin/fslval ${topupdir}/Pos_b0 dim3)
+		if [ $(isodd $dimz) -eq 1 ]; then
+			log_Msg "Input images have an odd number of slices. This is incompatible with the default topup configuration file."
+			log_Msg "Either supply a topup configuration file that doesn't use subsampling (e.g., FSL's 'b02b0_1.cnf') using the --topup-config-file=<file> flag (recommended)"
+			log_Msg "or instruct the HCP pipelines to remove a slice using the --ensure-even-slices flag (legacy option)."
+			log_Msg "Note that the legacy option is incompatible with slice-to-volume correction in FSL's eddy"
+			exit 1
+		fi
+	fi
+
 	# Create two files for each phase encoding direction, that for each series contain the number of
 	# corresponding volumes and the number of actual volumes. The file e.g. Pos_SeriesCorrespVolNum.txt
 	# will contain as many rows as non-EMPTY series. The entry M in row J indicates that volumes 0-M
@@ -490,8 +532,27 @@ main() {
 		${runcmd} ${HCPPIPEDIR_dMRI}/basic_preproc_sequence.sh ${outdir} ${ro_time} ${PEdir} ${b0dist} ${b0maxbval}
 	fi
 
+	if [ "${EnsureEvenSlices}" == "true" ]; then
+		topupdir=${outdir}/topup
+		eddydir=${outdir}/eddy
+		dimz=$(${FSLDIR}/bin/fslval ${topupdir}/Pos_b0 dim3)
+		if [ $(isodd $dimz) -eq 1 ]; then
+			echo "Removing one slice from data to get even number of slices"
+			for filename in Pos_Neg_b0 Pos_b0 Neg_b0 ; do
+				${FSLDIR}/bin/fslroi ${topupdir}/${filename} ${topupdir}/${filename}_tmp 0 -1 0 -1 1 -1
+				${FSLDIR}/bin/imrm ${topupdir}/${filename}
+				${FSLDIR}/bin/immv ${topupdir}/${filename}_tmp ${topupdir}/${filename}
+			done
+			${FSLDIR}/bin/fslroi ${eddydir}/Pos_Neg ${eddydir}/Pos_Neg_tmp 0 -1 0 -1 1 -1
+			${FSLDIR}/bin/imrm ${eddydir}/Pos_Neg
+			${FSLDIR}/bin/immv ${eddydir}/Pos_Neg_tmp ${eddydir}/Pos_Neg
+		else
+			echo "Skipping slice removal, because data already has an even number of slices"
+		fi
+	fi
+
 	log_Msg "Running Topup"
-	${runcmd} ${HCPPIPEDIR_dMRI}/run_topup.sh ${outdir}/topup
+	${runcmd} ${HCPPIPEDIR_dMRI}/run_topup.sh ${outdir}/topup ${TopupConfig}
 
 	log_Msg "Completed!"
 	exit 0

DiffusionPreprocessing/scripts/basic_preproc_best_b0.sh

@@ -13,10 +13,6 @@ echo "${scriptName}: Input Parameter: ro_time: ${ro_time}" # Readout time in sec
 echo "${scriptName}: Input Parameter: PEdir: ${PEdir}"
 echo "${scriptName}: Input Parameter: b0maxbval: ${b0maxbval}"
 
-isodd() {
-	echo "$(($1 % 2))"
-}
-
 rawdir=${workingdir}/rawdata
 topupdir=${workingdir}/topup
 eddydir=${workingdir}/eddy
@@ -223,7 +219,7 @@ elif [ ${PEdir} -eq 2 ]; then #AP/PA phase encoding
 fi
 
 ################################################################################################
-## Merging Files and correct number of slices
+## Merging Files
 ################################################################################################
 echo "Merging Pos and Neg images"
 ${FSLDIR}/bin/fslmerge -t ${rawdir}/Pos $(echo ${rawdir}/${basePos}_[0-9]*.nii*)
@@ -243,23 +239,6 @@ for idx in $(seq 1 $(${FSLDIR}/bin/fslval ${rawdir}/Neg dim4)); do
 	echo 2 >>${rawdir}/index.txt
 done
 
-dimz=$(${FSLDIR}/bin/fslval ${rawdir}/Pos dim3)
-if [ $(isodd $dimz) -eq 1 ]; then
-	echo "Remove one slice from data to get even number of slices"
-	${FSLDIR}/bin/fslroi ${rawdir}/Pos ${rawdir}/Posn 0 -1 0 -1 1 -1
-	${FSLDIR}/bin/fslroi ${rawdir}/Neg ${rawdir}/Negn 0 -1 0 -1 1 -1
-	${FSLDIR}/bin/fslroi ${rawdir}/best_Pos_b0 ${rawdir}/best_Pos_b0n 0 -1 0 -1 1 -1
-	${FSLDIR}/bin/fslroi ${rawdir}/best_Neg_b0 ${rawdir}/best_Neg_b0n 0 -1 0 -1 1 -1
-	${FSLDIR}/bin/imrm ${rawdir}/Pos
-	${FSLDIR}/bin/imrm ${rawdir}/Neg
-	${FSLDIR}/bin/imrm ${rawdir}/best_Pos_b0
-	${FSLDIR}/bin/imrm ${rawdir}/best_Neg_b0
-	${FSLDIR}/bin/immv ${rawdir}/Posn ${rawdir}/Pos
-	${FSLDIR}/bin/immv ${rawdir}/Negn ${rawdir}/Neg
-	${FSLDIR}/bin/immv ${rawdir}/best_Pos_b0n ${rawdir}/best_Pos_b0
-	${FSLDIR}/bin/immv ${rawdir}/best_Neg_b0n ${rawdir}/best_Neg_b0
-fi
-
 echo "Perform final merge"
 ${FSLDIR}/bin/fslmerge -t ${rawdir}/Pos_Neg_b0 ${rawdir}/best_Pos_b0 ${rawdir}/best_Neg_b0
 # include Pos_b0 as the first volume of Pos_Neg, so that eddy will use it as reference

DiffusionPreprocessing/scripts/basic_preproc_sequence.sh

@@ -14,9 +14,6 @@ echo "${scriptName}: Input Parameter: ro_time: ${ro_time}" # Readout time in sec
 echo "${scriptName}: Input Parameter: PEdir: ${PEdir}"
 echo "${scriptName}: Input Parameter: b0dist: ${b0dist}"
 echo "${scriptName}: Input Parameter: b0maxbval: ${b0maxbval}"
-isodd() {
-	echo "$(($1 % 2))"
-}
 
 rawdir=${workingdir}/rawdata
 topupdir=${workingdir}/topup
@@ -138,7 +135,7 @@ for entry in ${rawdir}/${baseNeg}_[0-9]*.nii*; do #For each Neg volume
 done
 
 ################################################################################################
-## Merging Files and correct number of slices
+## Merging Files
 ################################################################################################
 echo "Merging Pos and Neg images"
 ${FSLDIR}/bin/fslmerge -t ${rawdir}/Pos_b0 $(${FSLDIR}/bin/imglob ${rawdir}/Pos_b0_????.*)
@@ -153,23 +150,6 @@ paste $(echo ${rawdir}/${basePos}_[0-9]*.bvec) >${rawdir}/Pos.bvec
 paste $(echo ${rawdir}/${baseNeg}_[0-9]*.bval) >${rawdir}/Neg.bval
 paste $(echo ${rawdir}/${baseNeg}_[0-9]*.bvec) >${rawdir}/Neg.bvec
 
-dimz=$(${FSLDIR}/bin/fslval ${rawdir}/Pos dim3)
-if [ $(isodd $dimz) -eq 1 ]; then
-	echo "Remove one slice from data to get even number of slices"
-	${FSLDIR}/bin/fslroi ${rawdir}/Pos ${rawdir}/Posn 0 -1 0 -1 1 -1
-	${FSLDIR}/bin/fslroi ${rawdir}/Neg ${rawdir}/Negn 0 -1 0 -1 1 -1
-	${FSLDIR}/bin/fslroi ${rawdir}/Pos_b0 ${rawdir}/Pos_b0n 0 -1 0 -1 1 -1
-	${FSLDIR}/bin/fslroi ${rawdir}/Neg_b0 ${rawdir}/Neg_b0n 0 -1 0 -1 1 -1
-	${FSLDIR}/bin/imrm ${rawdir}/Pos
-	${FSLDIR}/bin/imrm ${rawdir}/Neg
-	${FSLDIR}/bin/imrm ${rawdir}/Pos_b0
-	${FSLDIR}/bin/imrm ${rawdir}/Neg_b0
-	${FSLDIR}/bin/immv ${rawdir}/Posn ${rawdir}/Pos
-	${FSLDIR}/bin/immv ${rawdir}/Negn ${rawdir}/Neg
-	${FSLDIR}/bin/immv ${rawdir}/Pos_b0n ${rawdir}/Pos_b0
-	${FSLDIR}/bin/immv ${rawdir}/Neg_b0n ${rawdir}/Neg_b0
-fi
-
 echo "Perform final merge"
 ${FSLDIR}/bin/fslmerge -t ${rawdir}/Pos_Neg_b0 ${rawdir}/Pos_b0 ${rawdir}/Neg_b0
 ${FSLDIR}/bin/fslmerge -t ${rawdir}/Pos_Neg ${rawdir}/Pos ${rawdir}/Neg

DiffusionPreprocessing/scripts/run_topup.sh

@@ -4,10 +4,7 @@ source "${HCPPIPEDIR}/global/scripts/debug.shlib" "$@" # Debugging functions; al
 echo -e "\n START: run_topup"
 
 workingdir=$1
-
-configdir=${HCPPIPEDIR_Config}
-#topup_config_file=${FSLDIR}/etc/flirtsch/b02b0.cnf
-topup_config_file=${configdir}/b02b0.cnf
+topup_config_file=$2
 
 ${FSLDIR}/bin/topup --imain=${workingdir}/Pos_Neg_b0 --datain=${workingdir}/acqparams.txt --config=${topup_config_file} --out=${workingdir}/topup_Pos_Neg_b0 -v --fout=${workingdir}/topup_Pos_Neg_b0_field.nii.gz