Hi Ammar,
Check these paths:
SpinEchoPhaseEncodeNegative="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_SpinEchoFieldMap_AP.nii.gz"
SpinEchoPhaseEncodePositive="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_SpinEchoFieldMap_PA.nii.gz”
Matt.
From: "Hawasli, Ammar" <hawas...@wustl.edu<mailto:hawas...@wustl.edu>>
Date: Tuesday, July 17, 2018 at 12:31 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] GradientDistortionUnwarp error help.
Here is the batch script
get_batch_options() {
local arguments=("$@")
unset command_line_specified_study_folder
unset command_line_specified_subj
unset command_line_specified_run_local
local index=0
local numArgs=${#arguments[@]}
local argument
while [ ${index} -lt ${numArgs} ]; do
argument=${arguments[index]}
case ${argument} in
--StudyFolder=*)
command_line_specified_study_folder=${argument#*=}
index=$(( index + 1 ))
;;
--Subject=*)
command_line_specified_subj=${argument#*=}
index=$(( index + 1 ))
;;
--runlocal)
command_line_specified_run_local="TRUE"
index=$(( index + 1 ))
;;
*)
echo ""
echo "ERROR: Unrecognized Option: ${argument}"
echo ""
exit 1
;;
esac
done
}
# Function: main
# Description: main processing work of this script
main()
{
get_batch_options "$@"
# Set variable values that locate and specify data to process
#StudyFolder="${HOME}/projects/Pipelines_ExampleData" # Location of Subject
folders (named by subjectID)
StudyFolder="${HOME}/Data/mystudy"
Subjlist="CON-015" # Space delimited list of subject IDs
# Set variable value that sets up environment
#EnvironmentScript="${HOME}/projects/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh"
# Pipeline environment script
EnvironmentScript="${HOME}/NecessaryDownloads/HCPpipelines-master/MySetUp.sh"
# Use any command line specified options to override any of the variable
settings above
if [ -n "${command_line_specified_study_folder}" ]; then
StudyFolder="${command_line_specified_study_folder}"
fi
if [ -n "${command_line_specified_subj}" ]; then
Subjlist="${command_line_specified_subj}"
fi
# Report major script control variables to user
echo "StudyFolder: ${StudyFolder}"
echo "Subjlist: ${Subjlist}"
echo "EnvironmentScript: ${EnvironmentScript}"
echo "Run locally: ${command_line_specified_run_local}"
# Set up pipeline environment variables and software
source ${EnvironmentScript}
# Define processing queue to be used if submitted to job scheduler
# if [ X$SGE_ROOT != X ] ; then
# QUEUE="-q long.q"
# QUEUE="-q veryshort.q"
QUEUE="-q hcp_priority.q"
# fi
# If PRINTCOM is not a null or empty string variable, then
# this script and other scripts that it calls will simply
# print out the primary commands it otherwise would run.
# This printing will be done using the command specified
# in the PRINTCOM variable
PRINTCOM=""
# PRINTCOM="echo"
#
# Inputs:
#
# Scripts called by this script do NOT assume anything about the form of the
# input names or paths. This batch script assumes the HCP raw data naming
# convention, e.g.
#
#
${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_T1w_MPR1.nii.gz
#
${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR2/${Subject}_3T_T1w_MPR2.nii.gz
#
#
${StudyFolder}/${Subject}/unprocessed/3T/T2w_SPC1/${Subject}_3T_T2w_SPC1.nii.gz
#
${StudyFolder}/${Subject}/unprocessed/3T/T2w_SPC2/${Subject}_3T_T2w_SPC2.nii.gz
#
#
${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_FieldMap_Magnitude.nii.gz
#
${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_FieldMap_Phase.nii.gz
# Scan settings:
#
# Change the Scan Settings (e.g. Sample Spacings and $UnwarpDir) to match
your
# structural images. These are set to match the HCP-YA ("Young Adult")
Protocol by default.
# (i.e., the study collected on the customized Connectom scanner).
# Readout Distortion Correction:
#
# You have the option of using either gradient echo field maps or spin echo
# field maps to perform readout distortion correction on your structural
# images, or not to do readout distortion correction at all.
#
# The HCP Pipeline Scripts currently support the use of gradient echo field
# maps or spin echo field maps as they are produced by the Siemens Connectom
# Scanner. They also support the use of gradient echo field maps as
generated
# by General Electric scanners.
#
# Change either the gradient echo field map or spin echo field map scan
# settings to match your data. This script is setup to use gradient echo
# field maps from the Siemens Connectom Scanner collected using the HCP-YA
Protocol.
# Gradient Distortion Correction:
#
# If using gradient distortion correction, use the coefficents from your
# scanner. The HCP gradient distortion coefficents are only available
through
# Siemens. Gradient distortion in standard scanners like the Trio is much
# less than for the HCP Connectom scanner.
# DO WORK
# Cycle through specified subjects
for Subject in $Subjlist ; do
echo $Subject
# Input Images
# Detect Number of T1w Images and build list of full paths to
# T1w images
numT1ws=`ls ${StudyFolder}/${Subject}/unprocessed/3T | grep 'T1w_MPR.$'
| wc -l`
echo "Found ${numT1ws} T1w Images for subject ${Subject}"
T1wInputImages=""
i=1
while [ $i -le $numT1ws ] ; do
T1wInputImages=`echo
"${T1wInputImages}${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR${i}/${Subject}_3T_T1w_MPR${i}.nii.gz@"`
i=$(($i+1))
done
# Detect Number of T2w Images and build list of full paths to
# T2w images
numT2ws=`ls ${StudyFolder}/${Subject}/unprocessed/3T | grep 'T2w_SPC.$'
| wc -l`
echo "Found ${numT2ws} T2w Images for subject ${Subject}"
T2wInputImages=""
i=1
while [ $i -le $numT2ws ] ; do
T2wInputImages=`echo
"${T2wInputImages}${StudyFolder}/${Subject}/unprocessed/3T/T2w_SPC${i}/${Subject}_3T_T2w_SPC${i}.nii.gz@"`
i=$(($i+1))
done
# Readout Distortion Correction:
#
# Currently supported Averaging and readout distortion correction
# methods: (i.e. supported values for the AvgrdcSTRING variable in
this
# script and the --avgrdcmethod= command line option for the
# PreFreeSurferPipeline.sh script.)
#
# "NONE"
# Average any repeats but do no readout distortion correction
#
# "FIELDMAP"
# This value is equivalent to the "SiemensFieldMap" value described
# below. Use of the "SiemensFieldMap" value is prefered, but
# "FIELDMAP" is included for backward compatibility with the
versions
# of these scripts that only supported use of Siemens-specific
# Gradient Echo Field Maps and did not support Gradient Echo Field
# Maps from any other scanner vendor.
#
# "TOPUP"
# Average any repeats and use Spin Echo Field Maps for readout
# distortion correction
#
# "GeneralElectricFieldMap"
# Average any repeats and use General Electric specific Gradient
# Echo Field Map for readout distortion correction
#
# "SiemensFieldMap"
# Average any repeats and use Siemens specific Gradient Echo
# Field Maps for readout distortion correction
#
# Current Setup is for Siemens specific Gradient Echo Field Maps
#
# The following settings for AvgrdcSTRING, MagnitudeInputName,
# PhaseInputName, and TE are for using the Siemens specific
# Gradient Echo Field Maps that are collected and used in the
# standard HCP-YA protocol.
#
# Note: The AvgrdcSTRING variable could also be set to the value
# "FIELDMAP" which is equivalent to "SiemensFieldMap".
#AvgrdcSTRING="SiemensFieldMap"
AvgrdcSTRING="TOPUP"
# ----------------------------------------------------------------------
# Variables related to using Siemens specific Gradient Echo Field Maps
# ----------------------------------------------------------------------
# The MagnitudeInputName variable should be set to a 4D magitude volume
# with two 3D timepoints or "NONE" if not used
#MagnitudeInputName="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_FieldMap_Magnitude.nii.gz"
MagnitudeInputName="NONE"
# The PhaseInputName variable should be set to a 3D phase difference
# volume or "NONE" if not used
#PhaseInputName="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_FieldMap_Phase.nii.gz"
PhaseInputName="NONE"
# The TE variable should be set to 2.46ms for 3T scanner, 1.02ms for 7T
# scanner or "NONE" if not using
#TE="2.46"
TE="NONE"
# ----------------------------------------------------------------------
# Variables related to using Spin Echo Field Maps
# ----------------------------------------------------------------------
# The following variables would be set to values other than "NONE" for
# using Spin Echo Field Maps (i.e. when AvgrdcSTRING="TOPUP")
# The SpinEchoPhaseEncodeNegative variable should be set to the
# spin echo field map volume with a negative phase encoding direction
# (LR if using a pair of LR/RL Siemens Spin Echo Field Maps (SEFMs);
# AP if using a pair of AP/PA Siemens SEFMS)
# and set to "NONE" if not using SEFMs
# (i.e. if AvgrdcSTRING is not equal to "TOPUP")
#
# Example values for when using Spin Echo Field Maps from a Siemens
machine:
#
${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_SpinEchoFieldMap_LR.nii.gz
#
${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_SpinEchoFieldMap_AP.nii.gz
#SpinEchoPhaseEncodeNegative="NONE"
SpinEchoPhaseEncodeNegative="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_SpinEchoFieldMap_AP.nii.gz"
# The SpinEchoPhaseEncodePositive variable should be set to the
# spin echo field map volume with positive phase encoding direction
# (RL if using a pair of LR/RL SEFMs; PA if using a AP/PA pair),
# and set to "NONE" if not using Spin Echo Field Maps
# (i.e. if AvgrdcSTRING is not equal to "TOPUP")
#
# Example values for when using Spin Echo Field Maps from a Siemens
machine:
#
${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_SpinEchoFieldMap_RL.nii.gz
#
${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_SpinEchoFieldMap_PA.nii.gz
SpinEchoPhaseEncodePositive="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_SpinEchoFieldMap_PA.nii.gz"
# Echo Spacing or Dwelltime of spin echo EPI MRI image. Specified in
seconds.
# Set to "NONE" if not used.
#
# Dwelltime = 1/(BandwidthPerPixelPhaseEncode * # of phase encoding
samples)
# DICOM field (0019,1028) = BandwidthPerPixelPhaseEncode
# DICOM field (0051,100b) = AcquisitionMatrixText first value (# of
phase encoding samples).
# On Siemens, iPAT/GRAPPA factors have already been accounted for.
#
# Example value for when using Spin Echo Field Maps:
# 0.000580002668012
DwellTime="0.00056"
# Spin Echo Unwarping Direction
# x or y (minus or not does not matter)
# "NONE" if not used
#
# Example values for when using Spin Echo Field Maps: x, -x, y, -y
# Note: +x or +y are not supported. For positive values, DO NOT include
the + sign
## MPH: Why do we say that "minus or not does not matter", but then
list -x and -y as example values??
SEUnwarpDir="y"
# Topup Configuration file
# "NONE" if not used
TopupConfig="b02b0"
# ----------------------------------------------------------------------
# Variables related to using General Electric specific Gradient Echo
# Field Maps
# ----------------------------------------------------------------------
# The following variables would be set to values other than "NONE" for
# using General Electric specific Gradient Echo Field Maps (i.e. when
# AvgrdcSTRING="GeneralElectricFieldMap")
# Example value for when using General Electric Gradient Echo Field Map
#
# GEB0InputName should be a General Electric style B0 fieldmap with two
# volumes
# 1) fieldmap in deg and
# 2) magnitude,
# set to NONE if using TOPUP or FIELDMAP/SiemensFieldMap
#
#
GEB0InputName="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_GradientEchoFieldMap.nii.gz"
GEB0InputName="NONE"
# Templates
# Hires T1w MNI template
T1wTemplate="${HCPPIPEDIR_Templates}/MNI152_T1_0.8mm.nii.gz"
# Hires brain extracted MNI template
T1wTemplateBrain="${HCPPIPEDIR_Templates}/MNI152_T1_0.8mm_brain.nii.gz"
# Lowres T1w MNI template
T1wTemplate2mm="${HCPPIPEDIR_Templates}/MNI152_T1_2mm.nii.gz"
# Hires T2w MNI Template
T2wTemplate="${HCPPIPEDIR_Templates}/MNI152_T2_0.8mm.nii.gz"
# Hires T2w brain extracted MNI Template
T2wTemplateBrain="${HCPPIPEDIR_Templates}/MNI152_T2_0.8mm_brain.nii.gz"
# Lowres T2w MNI Template
T2wTemplate2mm="${HCPPIPEDIR_Templates}/MNI152_T2_2mm.nii.gz"
# Hires MNI brain mask template
TemplateMask="${HCPPIPEDIR_Templates}/MNI152_T1_0.8mm_brain_mask.nii.gz"
# Lowres MNI brain mask template
Template2mmMask="${HCPPIPEDIR_Templates}/MNI152_T1_2mm_brain_mask_dil.nii.gz"
# Structural Scan Settings
#
# Note that "UnwarpDir" is the *readout* direction of the *structural*
(T1w,T2w)
# images, and should not be confused with "SEUnwarpDir" which is the
*phase* encoding direction
# of the Spin Echo Field Maps (if using them).
#
# set all these values to NONE if not doing readout distortion
correction
#
# Sample values for when using General Electric structurals
# T1wSampleSpacing="0.000011999" # For General Electric scanners,
1/((0018,0095)*(0028,0010))
# T2wSampleSpacing="0.000008000" # For General Electric scanners,
1/((0018,0095)*(0028,0010))
# UnwarpDir="y" ## MPH: This doesn't seem right. Is this accurate??
# The values set below are for the HCP-YA Protocol using the Siemens
# Connectom Scanner
# DICOM field (0019,1018) in s or "NONE" if not used
T1wSampleSpacing="0.0000021"
# DICOM field (0019,1018) in s or "NONE" if not used
T2wSampleSpacing="0.0000021"
# z appears to be the appropriate polarity for the 3D structurals
collected on Siemens scanners
# or "NONE" if not used
UnwarpDir="z"
# Other Config Settings
# BrainSize in mm, 150 for humans
BrainSize="150"
# FNIRT 2mm T1w Config
FNIRTConfig="${HCPPIPEDIR_Config}/T1_2_MNI152_2mm.cnf"
# Location of Coeffs file or "NONE" to skip
# GradientDistortionCoeffs="${HCPPIPEDIR_Config}/coeff_SC72C_Skyra.grad"
# Set to NONE to skip gradient distortion correction
#GradientDistortionCoeffs="NONE"
GradientDistortionCoeffs="${HOME}/NecessaryDownloads/HCPpipelines-master/coeff_AS82_Prisma.grad"
# Establish queuing command based on command line option
if [ -n "${command_line_specified_run_local}" ] ; then
echo "About to run
${HCPPIPEDIR}/PreFreeSurfer/PreFreeSurferPipeline.sh"
queuing_command=""
else
echo "About to use fsl_sub to queue or run
${HCPPIPEDIR}/PreFreeSurfer/PreFreeSurferPipeline.sh"
queuing_command="${FSLDIR}/bin/fsl_sub ${QUEUE}"
fi
# Run (or submit to be run) the PreFreeSurferPipeline.sh script
# with all the specified parameter values
${queuing_command} ${HCPPIPEDIR}/PreFreeSurfer/PreFreeSurferPipeline.sh
\
--path="$StudyFolder" \
--subject="$Subject" \
--t1="$T1wInputImages" \
--t2="$T2wInputImages" \
--t1template="$T1wTemplate" \
--t1templatebrain="$T1wTemplateBrain" \
--t1template2mm="$T1wTemplate2mm" \
--t2template="$T2wTemplate" \
--t2templatebrain="$T2wTemplateBrain" \
--t2template2mm="$T2wTemplate2mm" \
--templatemask="$TemplateMask" \
--template2mmmask="$Template2mmMask" \
--brainsize="$BrainSize" \
--fnirtconfig="$FNIRTConfig" \
--fmapmag="$MagnitudeInputName" \
--fmapphase="$PhaseInputName" \
--fmapgeneralelectric="$GEB0InputName" \
--echodiff="$TE" \
--SEPhaseNeg="$SpinEchoPhaseEncodeNegative" \
--SEPhasePos="$SpinEchoPhaseEncodePositive" \
--echospacing="$DwellTime" \
--seunwarpdir="$SEUnwarpDir" \
--t1samplespacing="$T1wSampleSpacing" \
--t2samplespacing="$T2wSampleSpacing" \
--unwarpdir="$UnwarpDir" \
--gdcoeffs="$GradientDistortionCoeffs" \
--avgrdcmethod="$AvgrdcSTRING" \
--topupconfig="$TopupConfig" \
--printcom=$PRINTCOM
done
}
# Invoke the main function to get things started
main "$@"
________________________________
From: Glasser, Matthew
Sent: Tuesday, July 17, 2018 12:24:27 PM
To: Steve Smith; Hawasli, Ammar
Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] GradientDistortionUnwarp error help.
Hi Ammar,
Please post your .bat call to the pipeline script. Most likely you need to set
somethings to NONE
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Steve Smith <st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk>>
Date: Tuesday, July 17, 2018 at 11:23 AM
To: "Hawasli, Ammar" <hawas...@wustl.edu<mailto:hawas...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] GradientDistortionUnwarp error help.
HI - looks like maybe the fieldmap inputs are not setup correctly?
Cheers.
On 17 Jul 2018, at 12:19, Hawasli, Ammar
<hawas...@wustl.edu<mailto:hawas...@wustl.edu>> wrote:
Hello All,
I am having a bug with my Gradient Distortion Unwarp process in prefreesurfer
and wanted to reach out for ideas.
This is what is shows:
START: GradientDistortionUnwarp
gradunwarp-INFO: Parsing
/mnt/md126p2/Ubuntu/home/functionalspinelab/NecessaryDownloads/HCPpipelines-master/coeff_AS82_Prisma.grad
for harmonics coeffs
gradunwarp-INFO: Evaluating spherical harmonics
gradunwarp-INFO: on a 60^3 grid
gradunwarp-INFO: with extents -300.0mm to 300.0mm
gradunwarp-INFO: along x...
gradunwarp-INFO: along y...
gradunwarp-INFO: along z...
gradunwarp-INFO: Evaluating the jacobian multiplier
gradunwarp-INFO: Unwarping slice by slice
. . . . . . . . . 10 . . . . . . . . . 20 . . . . . . . . . 30 . . . . . . . .
. 40 . . . . . . . . . 50 . . . . . . . . . 60 . . . . . . . . . 70 . . . . . .
. . . 80 . . . . . . . . . 90 . . . . . . . . . 100 . . . . . . . . . 110 . . .
. . . . . . 120 . . . . . . . . . 130 . . . . . . . . . 140 . . . . . . . . .
150 . . . . . . . . . 160 . . . . . . . . . 170 . . . . . . . . . 180 . . . . .
. . . . 190 . . . . . . . . . 200 . . . . . . . . . 210 . . . . . . . . . 220 .
. . . . . . . . 230 . . . . . . . . . 240 . . . . . . . . . 250 . . . . . . . .
. 260 . . . . . . . . . 270 . . . . . . . . . 280 . . . . . . . . . 290 . . . .
. . . . . 300 . . . . . . . . . 310 . . . . . . . . . 320
gradunwarp-INFO: Writing output to trilinear.nii.gz
END: GradientDistortionUnwarp
Mon Jul 16 15:21:59 CDT 2018 - PreFreeSurferPipeline.sh: Not Averaging T2w
Images
Mon Jul 16 15:21:59 CDT 2018 - PreFreeSurferPipeline.sh: ONLY ONE AVERAGE
FOUND: COPYING
Mon Jul 16 15:21:59 CDT 2018 - PreFreeSurferPipeline.sh: Aligning T2w image to
0.7mm MNI T2wTemplate to create native volume space
Mon Jul 16 15:21:59 CDT 2018 - PreFreeSurferPipeline.sh: mkdir -p
/mnt/md126p2/Ubuntu/home/functionalspinelab/Data/mystudy/CON-015/T2w/ACPCAlignment
START: ACPCAlignment
Final FOV is:
0.000000 208.000000 0.000000 300.000000 78.000000 188.000000
END: ACPCAlignment
Mon Jul 16 15:23:03 CDT 2018 - PreFreeSurferPipeline.sh: Performing Brain
Extraction using FNIRT-based Masking
Mon Jul 16 15:23:03 CDT 2018 - PreFreeSurferPipeline.sh: mkdir -p
/mnt/md126p2/Ubuntu/home/functionalspinelab/Data/mystudy/CON-015/T2w/BrainExtraction_FNIRTbased
START: BrainExtraction_FNIRT
END: BrainExtraction_FNIRT
Mon Jul 16 15:29:28 CDT 2018 - PreFreeSurferPipeline.sh: Performing TOPUP
Readout Distortion Correction
Mon Jul 16 15:29:28 CDT 2018 - PreFreeSurferPipeline.sh: mkdir -p
/mnt/md126p2/Ubuntu/home/functionalspinelab/Data/mystudy/CON-015/T2w/T2wToT1wDistortionCorrectAndReg
START: T2WToT1wDistortionCorrectAndReg.sh
Mon Jul 16 15:29:30 CDT 2018 - TopupPreprocessingAll.sh: START: Topup Field Map
Generation and Gradient Unwarping
ERROR: Could not open file
ERROR: Could not open file
ERROR: Could not open file
ERROR: Could not open file
START: GradientDistortionUnwarp
Cannot open volume
/mnt/md126p2/Ubuntu/home/functionalspinelab/Data/mystudy/CON-015/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/PhaseOne
for reading!
____________________
I am using a Prisma and have the new gradunwarp installed which has the bug fix
for global, siemens_cas value. I also obviously have my coefficient file
referenced normally.
Any ideas?
Thanks
Ammar
________________________________
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+44 (0) 1865 222726 (fax 222717)
st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk>
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________________________________
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
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