I would post this on the FSL list because Jesper would need to tell you what to do with your data.
Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Leonardo Tozzi <[email protected]<mailto:[email protected]>> Date: Wednesday, August 1, 2018 at 5:19 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Index error in diffusion preprocessing 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 _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ 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 mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
