[HCP-Users] Re: HCP pipeline for Lifespan Pilot Data

[Glasser, Matthew]

You need to set up the script appropriately meaning convert from standard field 
map to topup-based field map readout distortion correction, use appropriately 
sized templates, etc, so change these variables:

T1wInputImages="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_T1w_MPR1_gdc.nii.gz"
T2wInputImages="${StudyFolder}/${Subject}/unprocessed/3T/T2w_SPC1/${Subject}_3T_T2w_SPC1_gdc.nii.gz"

AvgrdcSTRING=“TOPUP"
MagnitudeInputName=“NONE"
PhaseInputName=“NONE"
TE=“NONE

SpinEchoPhaseEncodeNegative="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_SpinEchoFieldMap_LR_gdc.nii.gz"
SpinEchoPhaseEncodePositive="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_SpinEchoFieldMap_RL_gdc.nii.gz"
DwellTime="0.000580002668012"
SEUnwarpDir=“x"
TopupConfig="${HCPPIPEDIR_Config}/b02b0.cnf"

T1wTemplate="${HCPPIPEDIR_Templates}/MNI152_T1_0.8mm.nii.gz"
T1wTemplateBrain="${HCPPIPEDIR_Templates}/MNI152_T1_0.8mm_brain.nii.gz"
T2wTemplate="${HCPPIPEDIR_Templates}/MNI152_T2_0.8mm.nii.gz"
T2wTemplateBrain="${HCPPIPEDIR_Templates}/MNI152_T2_0.8mm_brain.nii.gz"
TemplateMask="${HCPPIPEDIR_Templates}/MNI152_T1_0.8mm_brain_mask.nii.gz”

You will need to make corresponding changes to the fMRIVolume Pipeline as well.

Matt.

From: 南 修司郎 <shujiromin...@me.com<mailto:shujiromin...@me.com>>
Date: Sunday, August 26, 2018 at 6:26 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] HCP pipeline for Lifespan Pilot Data

This is my PreFreeSurferPipelineBatch.sh file. Thank you.

Shujiro

#!/bin/bash

#~ND~FORMAT~MARKDOWN~
#~ND~START~
#
# # PreFreeSurferPipelineBatch.sh
#
# ## Copyright Notice
#
# Copyright (C) 2013-2018 The Human Connectome Project
#
# * Washington University in St. Louis
# * University of Minnesota
# * Oxford University
#
# ## Author(s)
#
# * Matthew F. Glasser, Department of Anatomy and Neurobiology,
# Washington University in St. Louis
# * Timothy B. Brown, Neuroinformatics Research Group,
# Washington University in St. Louis
#
# ## Product
#
# [Human Connectome Project][HCP] (HCP) Pipelines
#
# ## License
#
# See the 
[LICENSE](https://github.com/Washington-University/Pipelines/blob/master/LICENSE.md)
 file
#
# ## Description:
#
# Example script for running the Pre-FreeSurfer phase of the HCP Structural
# Preprocessing pipeline
#
# See [Glasser et al. 2013][GlasserEtAl].
#
# ## Prerequisites
#
# ### Installed software
#
# * FSL (version 5.0.6)
# * FreeSurfer (version 5.3.0-HCP)
# * gradunwarp (HCP version 1.0.2) - if doing gradient distortion correction
#
# ### Environment variables
#
# Should be set in script file pointed to by EnvironmentScript variable.
# See setting of the EnvironmentScript variable in the main() function
# below.
#
# * FSLDIR - main FSL installation directory
# * FREESURFER_HOME - main FreeSurfer installation directory
# * HCPPIPEDIR - main HCP Pipelines installation directory
# * CARET7DIR - main Connectome Workbench installation directory
# * PATH - must point to where gradient_unwarp.py is if doing gradient unwarping
#
# <!-- References -->
# [HCP]: http://www.humanconnectome.org
# [GlasserEtAl]: http://www.ncbi.nlm.nih.gov/pubmed/23668970
#
#~ND~END~

# Function: get_batch_options
# Description
#
# Retrieve the following command line parameter values if specified
#
# --StudyFolder= - primary study folder containing subject ID subdirectories
# --Subjlist= - quoted, space separated list of subject IDs on which
# to run the pipeline
# --runlocal - if specified (without an argument), processing is run
# on "this" machine as opposed to being submitted to a
# computing grid
#
# Set the values of the following global variables to reflect command
# line specified parameters
#
# command_line_specified_study_folder
# command_line_specified_subj_list
# command_line_specified_run_local
#
# These values are intended to be used to override any values set
# directly within this script file
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)
Subjlist="LS2001" # Space delimited list of subject IDs

# Set variable value that sets up environment
EnvironmentScript="${HOME}/projects/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh"
 # Pipeline environment script

# 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"

# ----------------------------------------------------------------------
# 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"

# 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"

# 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"

# ----------------------------------------------------------------------
# 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"

# 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="NONE"

# 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="NONE"

# 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="NONE"

# Topup Configuration file
# "NONE" if not used
TopupConfig="NONE"

# ----------------------------------------------------------------------
# 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_0.7mm.nii.gz"

# Hires brain extracted MNI template
T1wTemplateBrain="${HCPPIPEDIR_Templates}/MNI152_T1_0.7mm_brain.nii.gz"

# Lowres T1w MNI template
T1wTemplate2mm="${HCPPIPEDIR_Templates}/MNI152_T1_2mm.nii.gz"

# Hires T2w MNI Template
T2wTemplate="${HCPPIPEDIR_Templates}/MNI152_T2_0.7mm.nii.gz"

# Hires T2w brain extracted MNI Template
T2wTemplateBrain="${HCPPIPEDIR_Templates}/MNI152_T2_0.7mm_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_0.7mm_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="0.0000074"

# 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"

# 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 "$@"

2018年8月27日 08:16、"Glasser, Matthew" 
<glass...@wustl.edu<mailto:glass...@wustl.edu>>さんのメッセージ：

What is in your ./PreFreeSurferPipelineBatch.sh file?

Matt.

From: 南 修司郎 <shujiromin...@me.com<mailto:shujiromin...@me.com>>
Date: Sunday, August 26, 2018 at 6:14 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] HCP pipeline for Lifespan Pilot Data

I performed PrefreeSerferPipeline, and get the following message.

shujirominami@shujirominami-MacBookAir-Ubuntu:~/projects/Pipelines/Examples/Scripts$
 ./PreFreeSurferPipelineBatch.sh
StudyFolder: /home/shujirominami/projects/Pipelines_ExampleData
Subjlist: LS2001
EnvironmentScript: 
/home/shujirominami/projects/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh
Run locally:
This script must be SOURCED to correctly setup the environment prior to running 
any of the other HCP scripts contained here
LS2001
Found 1 T1w Images for subject LS2001
Found 1 T2w Images for subject LS2001
About to use fsl_sub to queue or run 
/home/shujirominami/projects/Pipelines/PreFreeSurfer/PreFreeSurferPipeline.sh
Cannot open volume 
/home/shujirominami/projects/Pipelines_ExampleData/LS2001/unprocessed/3T/T1w_MPR1/LS2001_3T_FieldMap_Magnitude
 for reading!

Shujiro

2018年8月27日 08:02、"Glasser, Matthew" 
<glass...@wustl.edu<mailto:glass...@wustl.edu>>さんのメッセージ：

What about your pipeline call?

Matt.

From: 南 修司郎 <shujiromin...@me.com<mailto:shujiromin...@me.com>>
Date: Sunday, August 26, 2018 at 6:00 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] HCP pipeline for Lifespan Pilot Data

The T1w_MPR1 file includes the followings. Thank you.

LS2001_3T_SpinEchoFieldMap_LR_gdc.nii.gz
LS2001_3T_SpinEchoFieldMap_RL.nii.gz
LS2001_3T_SpinEchoFieldMap_LR.nii.gz
LS2001_3T_T1w_MPR1_gdc.nii.gz
LS2001_3T_SpinEchoFieldMap_RL_gdc.nii.gz
LS2001_3T_T1w_MPR1.nii.gz

Shujiro

2018年8月27日 07:48、"Glasser, Matthew" 
<glass...@wustl.edu<mailto:glass...@wustl.edu>>さんのメッセージ：

List your pipeline call and the files you have available, as I don’t recall 
what was distributed in the pilot data.

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of 南 修司郎 <shujiromin...@me.com<mailto:shujiromin...@me.com>>
Date: Sunday, August 26, 2018 at 5:45 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] HCP pipeline for Lifespan Pilot Data

Dear HCP experts,

I am trying to perform HCP pipeline for the WU-Minn HCP Lifespan Pilot Data. 
The following error occurred, because WU-Minn HCP Lifespan Pilot Data doesn't 
have "FieldMap_Magnitude" file.

"Cannot open volume 
/home/shujirominami/projects/Pipelines_ExampleData/LS2001/unprocessed/3T/T1w_MPR1/LS2001_3T_FieldMap_Magnitude
 for reading!"

I'd like to appreciate if you could explain the solution.

Best regards.

Shujiro Minami M.D., Ph.D.
Dpt. of Otolaryngology National Tokyo Medical Center
2-5-1 Higashigaoka, Meguro, Tokyo 152-8902, Japan
E-mail shujiromin...@me.com<mailto:shujiromin...@me.com>

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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.



________________________________
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 
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