To Whom it may concern,
I am trying to run the diffusion processing portion of the pipeline on my data,
but it is failing in the eddy step with the following error message:
Wed Aug 1 11:13:12 PDT 2018 - run_eddy.sh:
/share/software/user/open/fsl/5.0.10/bin/eddy_openmp
--imain=/scratch/users/ltozzi/HCP_HCPformat/conn009/Diffusion/eddy/Pos_Neg
--mask=/scratch/users/ltozzi/HCP_HCPformat/conn009/Diffusion/eddy/nodif_brain_mask
--index=/scratch/users/ltozzi/HCP_HCPformat/conn009/Diffusion/eddy/index.txt
--acqp=/scratch/users/ltozzi/HCP_HCPformat/conn009/Diffusion/eddy/acqparams.txt
--bvecs=/scratch/users/ltozzi/HCP_HCPformat/conn009/Diffusion/eddy/Pos_Neg.bvecs
--bvals=/scratch/users/ltozzi/HCP_HCPformat/conn009/Diffusion/eddy/Pos_Neg.bvals
--fwhm=0
--topup=/scratch/users/ltozzi/HCP_HCPformat/conn009/Diffusion/topup/topup_Pos_Neg_b0
--out=/scratch/users/ltozzi/HCP_HCPformat/conn009/Diffusion/eddy/eddy_unwarped_images
--flm=quadratic
terminate called after throwing an instance of 'TOPUP::TopupFileIOException'
what(): TopupFileIO:: msg=TopupDatafileReader::ReadOutTime: Invalid index
/home/groups/leanew1/ltozzi/HCPPipeline_3.27.0_sherlock/DiffusionPreprocessing/scripts/run_eddy.sh:
line 380: 33608 Aborted ${eddy_command}
I suspect this is due to the fact that in my data the first volume is not a b0
(the last one is), since in DiffusionPreprocessingBatch.sh I found the
following comment:
# NOTE that PosData defines the reference space in 'topup' and 'eddy' AND it
is assumed that
# each scan series begins with a b=0 acquisition, so that the reference space
in both
# 'topup' and 'eddy' will be defined by the same (initial b=0) volume.
My question is, do you think this is the reason (i.e. the scripts don’t
automatically “reorder” the scans based on the bvals) and if so, what would be
the easiest way to modify them to pick a specific volume instead of the first
one to find the initial b0? I suspect this would involve editing
DiffusionPreprocessing/scripts/basic_preproc.sh, but I was wondering if you
could provide some pointers so make this edit as small as possible (I would
like to avoid “shuffling” my scans, bvals and bvecs before launching the
preprocessing).
Thank you very much.
Yours faithfully,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
[email protected]<mailto:[email protected]> | (650) 5615738
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