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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 <gregory.b...@hhchealth.org>
Date: Tuesday, December 9, 2014 at 12:29 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] error when processing more than 2 tasks with GenericfMRIVolume script 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 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. _______________________________________________ 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] 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
