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Yes it is the EPI phase encoding direction. The positive and negative phase encoding directions are conventional (see the notes next to the variables for the convention). Basically, you want them in the order that produces a field map whose signs look
like a regular field map (as opposed to looking the opposite of it). Then all that remains is to specify the EPI phase encoding direction. If you were to reverse the spin echo image order, you would also have to reverse the EPI phase encoding direction (then
the correction would still work fine, but the topup field map would not have the same +/- convention as a regular field map.
Peace,
Matt.
From: <Book>, Gregory <[email protected]>
Date: Tuesday, December 9, 2014 at 2:49 PM To: Matt Glasser <[email protected]>, "[email protected]" <[email protected]> Cc: "Brown, Tim" <[email protected]> Subject: RE: [HCP-Users] error when processing more than 2 tasks with GenericfMRIVolume script So the phase encoding list corresponds to the EPI encoding direction, not the spin echo direction. How does TopUp know the encoding directions of the spin echos? Does it assume the positive image is the same
encoding direction as the EPI and the negative image is the opposite direction? From: Glasser, Matthew [mailto:[email protected]]
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]> 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 $@ StudyFolder="/home/pipeline/onrc/data/pipeline/S3777AUX/4/HCPfMRI-dominoSkyra" Subjlist="analysis" EnvironmentScript="/opt/HCP/HCP/Examples/Scripts/SetUpHCPPipeline.sh" if [ -n "${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_tfMRI_EMOTION_LR.nii.gz # ${StudyFolder}/${Subject}/unprocessed/3T/tfMRI_EMOTION_LR/${Subject}_3T_tfMRI_EMOTION_LR_SBRef.nii.gz # ${StudyFolder}/${Subject}/unprocessed/3T/tfMRI_EMOTION_RL/${Subject}_3T_tfMRI_EMOTION_RL.nii.gz # ${StudyFolder}/${Subject}/unprocessed/3T/tfMRI_EMOTION_RL/${Subject}_3T_tfMRI_EMOTION_RL_SBRef.nii.gz # ${StudyFolder}/${Subject}/unprocessed/3T/tfMRI_EMOTION_LR/${Subject}_3T_SpinEchoFieldMap_LR.nii.gz # ${StudyFolder}/${Subject}/unprocessed/3T/tfMRI_EMOTION_LR/${Subject}_3T_SpinEchoFieldMap_RL.nii.gz # ${StudyFolder}/${Subject}/unprocessed/3T/tfMRI_EMOTION_RL/${Subject}_3T_SpinEchoFieldMap_LR.nii.gz # ${StudyFolder}/${Subject}/unprocessed/3T/tfMRI_EMOTION_RL/${Subject}_3T_SpinEchoFieldMap_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}/${Subject}_3T_${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}/${Subject}/unprocessed/3T/${fMRIName}/${Subject}_3T_SpinEchoFieldMap_LR.nii.gz" #For the spin echo field map volume with a negative phase encoding direction (LR
in HCP data, AP in 7T HCP data), set to NONE if using regular FIELDMAP SpinEchoPhaseEncodePositive="${StudyFolder}/${Subject}/unprocessed/3T/${fMRIName}/${Subject}_3T_SpinEchoFieldMap_RL.nii.gz" #For the spin echo field map volume with a positive phase encoding direction (RL
in HCP data, PA in 7T HCP data), set to NONE if using regular FIELDMAP MagnitudeInputName="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_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/${Subject}_3T_FieldMap_Phase.nii.gz" #Expects 3D phase difference volume or "NONE" if not used DeltaTE="NONE" #2.46ms for 3T, 1.02ms for 7T, set to NONE if using TOPUP FinalFMRIResolution="3" #Target final resolution of fMRI data. 2mm is recommended for 3T HCP data, 1.6mm for 7T HCP data (i.e. should match acquired resolution). Use 2.0 or 1.0 to avoid standard FSL templates #GradientDistortionCoeffs="${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]]
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]> We’ve 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 (we’ve 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/shop1/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/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/shop1/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/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-SMARTTEST/analysis/unprocessed/3T/shop1/analysis_3T_shop1_SBRef.nii.gz --SEPhaseNeg=/home/pipeline/onrc/data/pipeline/S8931EBN/2/HCPfMRI-SMARTTEST/analysis/unprocessed/3T/shop1/analysis_3T_SpinEchoFieldMap_LR.nii.gz
--SEPhasePos=/home/pipeline/onrc/data/pipeline/S8931EBN/2/HCPfMRI-SMARTTEST/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
_______________________________________________ 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
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- [HCP-Users] error when processing more than 2 tasks with ... Book, Gregory
- Re: [HCP-Users] error when processing more than 2 ta... Glasser, Matthew
- Re: [HCP-Users] error when processing more than ... Book, Gregory
- Re: [HCP-Users] error when processing more t... Glasser, Matthew
- Re: [HCP-Users] error when processing mo... Book, Gregory
- Re: [HCP-Users] error when processi... Glasser, Matthew
- Re: [HCP-Users] error when processing mo... Xu, Junqian
- Re: [HCP-Users] error when processi... Glasser, Matthew
- Re: [HCP-Users] error when proc... Xu, Junqian
- Re: [HCP-Users] error when processing more than 2 ta... Timothy B. Brown
