After a second thought, maybe convert the list to array specifically for the
comparison purpose so the rest of the pipeline script don’t need to be modified
to use array indexing.
Tasklist="domino0 domino1 domino2 domino3"
PhaseEncodinglist="y y- y y-“
TaskArray=($Tasklist)
PhaseEncodingArray=($PhaseEcondinglist)
nTaskArray=${#TaskArray[@]}
nPhaseEncodingArray=${#PhaseEncodingArray[@]}
if [ $nTaskArray -ne $nPhaseEncodingArray ]; then
<Error message>
fi
Gordon
> On Dec 9, 2014, at 4:05 PM, Glasser, Matthew <[email protected]> wrote:
>
> Thanks Gordon, that would help too.
>
> On 12/9/14, 3:03 PM, "Xu, Junqian" <[email protected]> wrote:
>
>> Tim,
>>
>> A patch here to use array instead of space delimited string might be
>> helpful for error detection:
>>
>> e.g.
>>
>> Tasklist=(domino0 domino1 domino2 domino3)
>> PhaseEncodinglist=(y y- y y-)
>>
>> nTasklist=${#Tasklist[@]}
>> nPhaseEncodinglist=${#PhaseEncodinglist[@]}
>>
>> if [ $nTasklist -ne $nPhaseEncodinglist ]; then
>> <Error message>
>> fi
>>
>>
>> Gordon
>>
>>> On Dec 9, 2014, at 3:33 PM, Glasser, Matthew <[email protected]>
>>> wrote:
>>>
>>> You need to expand the PhaseEncodinglist variable to have the same
>>> length as the Tasklist variable (i.e. same number of elements separated
>>> by spaces). This probably should be made clearer in the comments for
>>> these variables.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: <Book>, Gregory <[email protected]>
>>> Date: Tuesday, December 9, 2014 at 2:19 PM
>>> To: Matt Glasser <[email protected]>,
>>> "[email protected]" <[email protected]>
>>> Subject: RE: [HCP-Users] error when processing more than 2 tasks with
>>> GenericfMRIVolume script
>>>
>>> Thanks, the script is attached. Also the directory structure is after
>>> the script.
>>>
>>> #!/bin/bash
>>>
>>> get_batch_options() {
>>> local arguments=($@)
>>>
>>> unset command_line_specified_study_folder
>>> unset command_line_specified_subj_list
>>> 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=$(( index + 1 ))
>>> ;;
>>> --Subjlist=*)
>>> command_line_specified_subj_list=${argument/*=/""}
>>> index=$(( index + 1 ))
>>> ;;
>>> --runlocal)
>>> command_line_specified_run_local="TRUE"
>>> index=$(( index + 1 ))
>>> ;;
>>> esac
>>> done
>>> }
>>>
>>> get_batch_options $@
>>>
>>>
>>> StudyFolder="/home/pipeline/onrc/data/pipeline/S3777AUX/4/HCPfMRI-dominoS
>>> kyra"
>>> Subjlist="analysis"
>>> EnvironmentScript="/opt/HCP/HCP/Examples/Scripts/SetUpHCPPipeline.sh"
>>>
>>> if [ -n "${command_line_specified_study_folder}" ]; then
>>> StudyFolder="${command_line_specified_study_folder}"
>>> fi
>>>
>>> if [ -n "${command_line_specified_subj_list}" ]; then
>>> Subjlist="${command_line_specified_subj_list}"
>>> fi
>>>
>>> # Requirements for this script
>>> # installed versions of: FSL (version 5.0.6), FreeSurfer (version
>>> 5.3.0-HCP) , gradunwarp (HCP version 1.0.1)
>>> # environment: FSLDIR , FREESURFER_HOME , HCPPIPEDIR , CARET7DIR ,
>>> PATH (for gradient_unwarp.py)
>>>
>>> #Set up pipeline environment variables and software
>>> . ${EnvironmentScript}
>>>
>>> # Log the originating call
>>> echo "$@"
>>>
>>> #if [ X$SGE_ROOT != X ] ; then
>>> QUEUE="-q long.q"
>>> #fi
>>>
>>> PRINTCOM=""
>>> #PRINTCOM="echo"
>>> #QUEUE="-q veryshort.q"
>>>
>>> ########################################## 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. for
>>> tfMRI_EMOTION_LR and tfMRI_EMOTION_RL:
>>>
>>> #
>>> ${StudyFolder}/${Subject}/unprocessed/3T/tfMRI_EMOTION_LR/${Subject}_3T_t
>>> fMRI_EMOTION_LR.nii.gz
>>> #
>>> ${StudyFolder}/${Subject}/unprocessed/3T/tfMRI_EMOTION_LR/${Subject}_3T_t
>>> fMRI_EMOTION_LR_SBRef.nii.gz
>>>
>>> #
>>> ${StudyFolder}/${Subject}/unprocessed/3T/tfMRI_EMOTION_RL/${Subject}_3T_t
>>> fMRI_EMOTION_RL.nii.gz
>>> #
>>> ${StudyFolder}/${Subject}/unprocessed/3T/tfMRI_EMOTION_RL/${Subject}_3T_t
>>> fMRI_EMOTION_RL_SBRef.nii.gz
>>>
>>> #
>>> ${StudyFolder}/${Subject}/unprocessed/3T/tfMRI_EMOTION_LR/${Subject}_3T_S
>>> pinEchoFieldMap_LR.nii.gz
>>> #
>>> ${StudyFolder}/${Subject}/unprocessed/3T/tfMRI_EMOTION_LR/${Subject}_3T_S
>>> pinEchoFieldMap_RL.nii.gz
>>>
>>> #
>>> ${StudyFolder}/${Subject}/unprocessed/3T/tfMRI_EMOTION_RL/${Subject}_3T_S
>>> pinEchoFieldMap_LR.nii.gz
>>> #
>>> ${StudyFolder}/${Subject}/unprocessed/3T/tfMRI_EMOTION_RL/${Subject}_3T_S
>>> pinEchoFieldMap_RL.nii.gz
>>>
>>> #Change Scan Settings: Dwelltime, FieldMap Delta TE (if using), and
>>> $PhaseEncodinglist to match your images
>>> #These are set to match the HCP Protocol by default
>>>
>>> #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 Skyra.
>>>
>>> #To get accurate EPI distortion correction with TOPUP, the flags in
>>> PhaseEncodinglist must match the phase encoding
>>> #direction of the EPI scan, and you must have used the correct images
>>> in SpinEchoPhaseEncodeNegative and Positive
>>> #variables. If the distortion is twice as bad as in the original
>>> images, flip either the order of the spin echo
>>> #images or reverse the phase encoding list flag. The pipeline expects
>>> you to have used the same phase encoding
>>> #axis in the fMRI data as in the spin echo field map data (x/-x or
>>> y/-y).
>>>
>>> ######################################### DO WORK
>>> ##########################################
>>>
>>> Tasklist=" domino0 domino1 domino2 domino3"
>>> PhaseEncodinglist="y y-"
>>>
>>> for Subject in $Subjlist ; do
>>> echo $Subject
>>>
>>> i=1
>>> for fMRIName in $Tasklist ; do
>>> echo " ${fMRIName}"
>>> UnwarpDir=`echo $PhaseEncodinglist | cut -d " " -f $i`
>>>
>>> fMRITimeSeries="${StudyFolder}/${Subject}/unprocessed/3T/${fMRIName}/${Su
>>> bject}_3T_${fMRIName}.nii.gz"
>>>
>>> fMRISBRef="${StudyFolder}/${Subject}/unprocessed/3T/${fMRIName}/${Subject
>>> }_3T_${fMRIName}_SBRef.nii.gz" #A single band reference image (SBRef) is
>>> recommended if using multiband, set to NONE if you want to use the first
>>> volume of the timeseries for motion correction
>>> DwellTime="0.00055" #Echo Spacing or Dwelltime of fMRI image, set
>>> to NONE if not used. Dwelltime = 1/(BandwidthPerPixelPhaseEncode * # of
>>> phase encoding samples): DICOM field (0019,1028) =
>>> BandwidthPerPixelPhaseEncode, DICOM field (0051,100b)
>>> AcquisitionMatrixText first value (# of phase encoding samples). On
>>> Siemens, iPAT/GRAPPA factors have already been accounted for.
>>> DistortionCorrection="TOPUP" #FIELDMAP or TOPUP, distortion
>>> correction is required for accurate processing
>>>
>>> SpinEchoPhaseEncodeNegative="${StudyFolder}/${Subject}/unprocessed/3T/${f
>>> MRIName}/${Subject}_3T_SpinEchoFieldMap_LR.nii.gz" #For the spin echo
>>> field map volume with a negative phase encoding direction (LR in HCP
>>> data, AP in 7T HCP data), set to NONE if using regular FIELDMAP
>>>
>>> SpinEchoPhaseEncodePositive="${StudyFolder}/${Subject}/unprocessed/3T/${f
>>> MRIName}/${Subject}_3T_SpinEchoFieldMap_RL.nii.gz" #For the spin echo
>>> field map volume with a positive phase encoding direction (RL in HCP
>>> data, PA in 7T HCP data), set to NONE if using regular FIELDMAP
>>>
>>> MagnitudeInputName="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${S
>>> ubject}_3T_FieldMap_Magnitude.nii.gz" #Expects 4D magitude volume with
>>> two 3D timepoints or "NONE" if not used
>>>
>>> PhaseInputName="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subje
>>> ct}_3T_FieldMap_Phase.nii.gz" #Expects 3D phase difference volume or
>>> "NONE" if not used
>>> DeltaTE="NONE" #2.46ms for 3T, 1.02ms for 7T, set to NONE if using
>>> TOPUP
>>> FinalFMRIResolution="3" #Target final resolution of fMRI data. 2mm
>>> is recommended for 3T HCP data, 1.6mm for 7T HCP data (i.e. should match
>>> acquired resolution). Use 2.0 or 1.0 to avoid standard FSL templates
>>>
>>> #GradientDistortionCoeffs="${HCPPIPEDIR_Config}/coeff_SC72C_Skyra.grad"
>>> #Gradient distortion correction coefficents, set to NONE to turn off
>>> GradientDistortionCoeffs="/opt/HCP/coeff_AS098.grad"
>>> TopUpConfig="${HCPPIPEDIR_Config}/b02b0.cnf" #Topup config if using
>>> TOPUP, set to NONE if using regular FIELDMAP
>>>
>>> if [ -n "${command_line_specified_run_local}" ] ; then
>>> echo "About to run
>>> ${HCPPIPEDIR}/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh"
>>> queuing_command=""
>>> else
>>> echo "About to use fsl_sub to queue or run
>>> ${HCPPIPEDIR}/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh"
>>> queuing_command="${FSLDIR}/bin/fsl_sub ${QUEUE}"
>>> fi
>>>
>>> ${queuing_command}
>>> ${HCPPIPEDIR}/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh \
>>> --path=$StudyFolder \
>>> --subject=$Subject \
>>> --fmriname=$fMRIName \
>>> --fmritcs=$fMRITimeSeries \
>>> --fmriscout=$fMRISBRef \
>>> --SEPhaseNeg=$SpinEchoPhaseEncodeNegative \
>>> --SEPhasePos=$SpinEchoPhaseEncodePositive \
>>> --fmapmag=$MagnitudeInputName \
>>> --fmapphase=$PhaseInputName \
>>> --echospacing=$DwellTime \
>>> --echodiff=$DeltaTE \
>>> --unwarpdir=$UnwarpDir \
>>> --fmrires=$FinalFMRIResolution \
>>> --dcmethod=$DistortionCorrection \
>>> --gdcoeffs=$GradientDistortionCoeffs \
>>> --topupconfig=$TopUpConfig \
>>> --printcom=$PRINTCOM
>>>
>>> # The following lines are used for interactive debugging to set the
>>> positional parameters: $1 $2 $3 ...
>>>
>>> echo "set -- --path=$StudyFolder \
>>> --subject=$Subject \
>>> --fmriname=$fMRIName \
>>> --fmritcs=$fMRITimeSeries \
>>> --fmriscout=$fMRISBRef \
>>> --SEPhaseNeg=$SpinEchoPhaseEncodeNegative \
>>> --SEPhasePos=$SpinEchoPhaseEncodePositive \
>>> --fmapmag=$MagnitudeInputName \
>>> --fmapphase=$PhaseInputName \
>>> --echospacing=$DwellTime \
>>> --echodiff=$DeltaTE \
>>> --unwarpdir=$UnwarpDir \
>>> --fmrires=$FinalFMRIResolution \
>>> --dcmethod=$DistortionCorrection \
>>> --gdcoeffs=$GradientDistortionCoeffs \
>>> --topupconfig=$TopUpConfig \
>>> --printcom=$PRINTCOM"
>>>
>>> echo ". ${EnvironmentScript}"
>>>
>>> i=$(($i+1))
>>> done
>>> done
>>>
>>>
>>> /analysis/unprocessed/3T/T1w_MPR1/analysis_3T_FieldMap_Magnitude.nii.gz
>>> Nov 24, 2014 14:10:03 rwxrwxrwx 490,268
>>> /analysis/unprocessed/3T/T1w_MPR1/analysis_3T_FieldMap_Phase.nii.gz
>>> Nov 24, 2014 14:10:03 rwxrwxrwx 500,252
>>> /analysis/unprocessed/3T/T1w_MPR1/analysis_3T_T1w_MPR1.nii.gz Nov
>>> 24, 2014 14:10:03 rwxrwxrwx 13,474,708
>>> /analysis/unprocessed/3T/T1w_MPR2/analysis_3T_T1w_MPR2.nii.gz Nov
>>> 24, 2014 14:10:04 rwxrwxrwx 13,446,820
>>> /analysis/unprocessed/3T/T1w_MPR3/analysis_3T_T1w_MPR3.nii.gz Nov
>>> 24, 2014 14:10:04 rwxrwxrwx 13,432,074
>>> /analysis/unprocessed/3T/T1w_MPR4/analysis_3T_T1w_MPR4.nii.gz Nov
>>> 24, 2014 14:10:05 rwxrwxrwx 13,393,346
>>> /analysis/unprocessed/3T/T1w_MPR5/analysis_3T_T1w_MPR5.nii.gz Nov
>>> 24, 2014 14:10:05 rwxrwxrwx 13,398,238
>>> /analysis/unprocessed/3T/T2w_SPC1/analysis_3T_T2w_SPC1.nii.gz
>>> Nov 24, 2014 14:10:06 rwxrwxrwx 8,551,575
>>> /analysis/unprocessed/3T/domino0/analysis_3T_SpinEchoFieldMap_LR.nii.gz
>>> Dec 9, 2014 15:52:11 rwxr-xr-x 1,119,399
>>> /analysis/unprocessed/3T/domino0/analysis_3T_SpinEchoFieldMap_RL.nii.gz
>>> Dec 9, 2014 15:52:11 rwxr-xr-x 1,127,080
>>> /analysis/unprocessed/3T/domino0/analysis_3T_domino0.nii.gz
>>> Dec 9, 2014 15:51:37 rwxr-xr-x 486,903,684
>>> /analysis/unprocessed/3T/domino0/analysis_3T_domino0_SBRef.nii.gz
>>> Dec 9, 2014 15:52:10 rwxr-xr-x 446,348
>>> /analysis/unprocessed/3T/domino1/analysis_3T_SpinEchoFieldMap_LR.nii.gz
>>> Dec 9, 2014 15:52:11 rwxr-xr-x 1,119,399
>>> /analysis/unprocessed/3T/domino1/analysis_3T_SpinEchoFieldMap_RL.nii.gz
>>> Dec 9, 2014 15:52:11 rwxr-xr-x 1,127,080
>>> /analysis/unprocessed/3T/domino1/analysis_3T_domino1.nii.gz
>>> Dec 9, 2014 15:51:46 rwxr-xr-x 488,162,639
>>> /analysis/unprocessed/3T/domino1/analysis_3T_domino1_SBRef.nii.gz
>>> Dec 9, 2014 15:52:11 rwxr-xr-x 447,898
>>> /analysis/unprocessed/3T/domino2/analysis_3T_SpinEchoFieldMap_LR.nii.gz
>>> Dec 9, 2014 15:52:11 rwxr-xr-x 1,119,399
>>> /analysis/unprocessed/3T/domino2/analysis_3T_SpinEchoFieldMap_RL.nii.gz
>>> Dec 9, 2014 15:52:11 rwxr-xr-x 1,127,080
>>> /analysis/unprocessed/3T/domino2/analysis_3T_domino2.nii.gz
>>> Dec 9, 2014 15:51:58 rwxr-xr-x 486,336,577
>>> /analysis/unprocessed/3T/domino2/analysis_3T_domino2_SBRef.nii.gz
>>> Dec 9, 2014 15:52:11 rwxr-xr-x 447,153
>>> /analysis/unprocessed/3T/domino3/analysis_3T_SpinEchoFieldMap_LR.nii.gz
>>> Dec 9, 2014 15:52:11 rwxr-xr-x 1,119,399
>>> /analysis/unprocessed/3T/domino3/analysis_3T_SpinEchoFieldMap_RL.nii.gz
>>> Dec 9, 2014 15:52:12 rwxr-xr-x 1,127,080
>>> /analysis/unprocessed/3T/domino3/analysis_3T_domino3.nii.gz
>>> Dec 9, 2014 15:52:10 rwxr-xr-x 484,561,229
>>> /analysis/unprocessed/3T/domino3/analysis_3T_domino3_SBRef.nii.gz
>>> Dec 9, 2014 15:52:11 rwxr-xr-x 445,265
>>>
>>> From: Glasser, Matthew
>>> [https://urldefense.proofpoint.com/v2/url?u=http-3A__mailto-3Aglasserm-40wusm.wustl.edu&d=AAIFAw&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=3I6-yvEg8KFim9hIErhCvm3QH8yehzFWJ6HsWQoeUT8&m=462KvT95ZwY2GnrxUDYMACjWW6bqjxJb-bL2VZbOrUM&s=IfZTeVUltm33ZMY9tUfEfEh6Rbi6GNsya5R-0U3YD58&e=
>>> ]
>>> Sent: Tuesday, December 09, 2014 2:43 PM
>>> To: Book, Gregory; [email protected]
>>> Subject: Re: [HCP-Users] error when processing more than 2 tasks with
>>> GenericfMRIVolume script
>>>
>>> Can you post the text of your launcher script? Only one task is run at
>>> a time inside the pipeline, so the issue will be there.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: <Book>, Gregory <[email protected]>
>>> Date: Tuesday, December 9, 2014 at 12:29 PM
>>> To: "[email protected]" <[email protected]>
>>> Subject: [HCP-Users] error when processing more than 2 tasks with
>>> GenericfMRIVolume script
>>>
>>> We¹ve run into a weird problem when using the GenericfMRIVolume batch
>>> script to process more than 2 tasks at a time. When we setup any more
>>> than 2 tasks (we¹ve tried 3 and 4 tasks), the first 2 run correctly and
>>> without error, but any after that crash in the TopUp section with the
>>> following error (the failed tasks all get to the same point):
>>>
>>> # RUN TOPUP
>>> # Needs FSL (version 5.0.6)
>>> ${FSLDIR}/bin/topup --imain=${WD}/BothPhases --datain=$txtfname
>>> --config=${TopupConfig} --out=${WD}/Coefficents --iout=${WD}/Magnitudes
>>> --fout=${WD}/TopupField --dfout=${WD}/WarpField
>>> --rbmout=${WD}/MotionMatrix --jacout=${WD}/Jacobian -v
>>> Could not open matrix file
>>> /home/pipeline/onrc/data/pipeline/S8931EBN/2/HCPfMRI-SMARTTEST/analysis/s
>>> hop1/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/Fie
>>> ldMap/acqparams.txt
>>>
>>> Part of FSL (build 506)
>>> topup
>>>
>>> Usage:
>>> topup --imain= --datain= --config= --coutname=my_field
>>>
>>>
>>> Compulsory arguments (You MUST set one or more of):
>>> --imain name of 4D file with images
>>> --datain name of text file with PE
>>> directions/times
>>>
>>> Optional arguments (You may optionally specify one or more of):
>>> --out base-name of output files
>>> (spline coefficients (Hz) and movement parameters)
>>> --fout name of image file with field
>>> (Hz)
>>> --iout name of 4D image file with
>>> unwarped images
>>> --logout Name of log-file
>>> --warpres (approximate) resolution (in mm)
>>> of warp basis for the different sub-sampling levels, default 10
>>> --subsamp sub-sampling scheme, default 1
>>> --fwhm FWHM (in mm) of gaussian
>>> smoothing kernel, default 8
>>> --config Name of config file specifying
>>> command line arguments
>>> --miter Max # of non-linear
>>> iterations, default 5
>>> --lambda Weight of regularisation, default
>>> depending on --ssqlambda and --regmod switches. See user documetation.
>>> --ssqlambda If set (=1), lambda is weighted by
>>> current ssq, default 1
>>> --regmod Model for regularisation of
>>> warp-field [membrane_energy bending_energy], default bending_energy
>>> --estmov Estimate movements if set, default
>>> 1 (true)
>>> --minmet Minimisation method
>>> 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient, default 0 (LM)
>>> --splineorder Order of spline, 2->Qadratic spline,
>>> 3->Cubic spline. Default=3
>>> --numprec Precision for representing Hessian,
>>> double or float. Default double
>>> --interp Image interpolation model,
>>> linear or spline. Default spline
>>> --scale If set (=1), the images are
>>> individually scaled to a common mean, default 0 (false)
>>> --regrid If set (=1), the calculations
>>> are done in a different grid, default 1 (true)
>>> -h,--help display help info
>>> -v,--verbose Print diagonostic information while
>>> running
>>> -h,--help display help info
>>>
>>>
>>>
>>> TopupFileIO:: msg=TopupDatafileReader:: error reading file
>>> /home/pipeline/onrc/data/pipeline/S8931EBN/2/HCPfMRI-SMARTTEST/analysis/s
>>> hop1/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/Fie
>>> ldMap/acqparams.txt
>>> set --
>>> --path=/home/pipeline/onrc/data/pipeline/S8931EBN/2/HCPfMRI-SMARTTEST
>>> --subject=analysis --fmriname=shop1
>>> --fmritcs=/home/pipeline/onrc/data/pipeline/S8931EBN/2/HCPfMRI-SMARTTEST/
>>> analysis/unprocessed/3T/shop1/analysis_3T_shop1.nii.gz
>>> --fmriscout=/home/pipeline/onrc/data/pipeline/S8931EBN/2/HCPfMRI-SMARTTES
>>> T/analysis/unprocessed/3T/shop1/analysis_3T_shop1_SBRef.nii.gz
>>> --SEPhaseNeg=/home/pipeline/onrc/data/pipeline/S8931EBN/2/HCPfMRI-SMARTTE
>>> ST/analysis/unprocessed/3T/shop1/analysis_3T_SpinEchoFieldMap_LR.nii.gz
>>>
>>> --SEPhasePos=/home/pipeline/onrc/data/pipeline/S8931EBN/2/HCPfMRI-SMARTTE
>>> ST/analysis/unprocessed/3T/shop1/analysis_3T_SpinEchoFieldMap_RL.nii.gz
>>> --fmapmag=NONE --fmapphase=NONE --echospacing=0.00055
>>> --echodiff=NONE --unwarpdir= --fmrires=2
>>> --dcmethod=TOPUP --gdcoeffs=/opt/HCP/coeff_AS098.grad
>>> --topupconfig=/opt/HCP/HCP/global/config/b02b0.cnf --printcom=
>>> . /opt/HCP/HCP/Examples/Scripts/SetUpHCPPipeline.sh
>>>
>>> _________________________________________________
>>> Gregory Book
>>> Senior Technology Manager
>>> Olin Neuropsychiatry Research Center, Institute of Living, Hartford
>>> Hospital
>>> 200 Retreat Avenue
>>> Hartford, CT 06106
>>> Tel: 860-545-7267 Fax: 860-545-7797
>>> [email protected]
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__nidb.sourceforge.net_&d=AAIFAw&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=3I6-yvEg8KFim9hIErhCvm3QH8yehzFWJ6HsWQoeUT8&m=462KvT95ZwY2GnrxUDYMACjWW6bqjxJb-bL2VZbOrUM&s=pvocyEuuzeMZkXyyQhEgQm3Ul25OazBHkawedG_9_N8&e=
>>>
>>>
>>>
>>> This e-mail message, including any attachments, is for the sole use of
>>> the intended recipient(s) and may contain confidential and privileged
>>> information. Any unauthorized review, use, disclosure, or distribution
>>> is prohibited. If you are not the intended recipient, or an employee or
>>> agent responsible for delivering the message to the intended recipient,
>>> please contact the sender by reply e-mail and destroy all copies of the
>>> original message, including any attachments.
>>> _______________________________________________
>>> HCP-Users mailing list
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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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>>>
>>> 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.
>>> _______________________________________________
>>> HCP-Users mailing list
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>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=AAIFAw&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=3I6-yvEg8KFim9hIErhCvm3QH8yehzFWJ6HsWQoeUT8&m=462KvT95ZwY2GnrxUDYMACjWW6bqjxJb-bL2VZbOrUM&s=XRvzeh5d7cj3gCjTQTLIS04j6AAbFQfHkzOFyL7Z4jY&e=
>>>
>>>
>>
>
>
> ________________________________
> The materials in this message are private and may contain Protected
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