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
[email protected]<mailto:[email protected]>
http://nidb.sourceforge.net
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