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 [mailto:[email protected]]
>> 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]
>> http://nidb.sourceforge.net
>>
>>
>> This e-mail message, including any attachments, is for the sole use of
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>>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.
>> _______________________________________________
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>>
>>
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>>received this email in error, please immediately notify the sender via
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>>
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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
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or the taking of any action in reliance on the contents of this information is
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