HCPpipelines eddy_postproc.sh Error

[Wenlan Zhang]

Dear HCP experts, 

I am hoping to run the Diffusion Preprocessing pipelines on one subject (subject HCD0042420) from the HCP-D dataset. Currently, I am doing non-GPU enabled eddy and gradient nonlinearity distortion correction. The pre-Eddy and Eddy steps seem to have gone well, however I am getting an error at the post processing step (the first error message is highlighted in yellow): 

START: eddy_postproc

Generating eddy QC report in /local_raid/data/HCPD/HCPpipelines-master/testdata/HCD0042420_V1_MR/Diffusion/QC

Traceback (most recent call last):

  File "/export01/local/fsl/bin/eddy_quad", line 54, in <module>

    main(args.eddyBase, args.eddyIdx, args.eddyParams, args.mask, args.bvals, args.bvecs, args.output_dir, args.field, args.slspec, args.verbose)

  File "/export01/local/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/eddy_qc/QUAD/quad.py", line 63, in main

    raise ValueError(eddyBase + ' does not appear to be a valid EDDY output basename')

ValueError: /local_raid/data/HCPD/HCPpipelines-master/testdata/HCD0042420_V1_MR/Diffusion/eddy/eddy_unwarped_images does not appear to be a valid EDDY output basename

Thu Jul  8 15:43:13 EDT 2021:eddy_postproc.sh: While running '/local_raid/data/HCPD/HCPpipelines-master/DiffusionPreprocessing/scripts/eddy_postproc.sh /local_raid/data/HCPD/HCPpipelines-master/testdata/HCD0042420_V1_MR/Diffusion /local_raid/data/HCPD/HCPpipelines-master/global/config/coeff_AS82.grad 1 0':

Thu Jul  8 15:43:13 EDT 2021:eddy_postproc.sh: ERROR: '/export01/local/fsl/bin/eddy_quad' command failed with return code: 1

Thu Jul  8 15:43:13 EDT 2021:eddy_postproc.sh: ERROR: '/export01/local/fsl/bin/eddy_quad' command failed with return code: 1

===> ERROR: Command returned with nonzero exit code

---------------------------------------------------

         script: eddy_postproc.sh

stopped at line: 35

           call: "${qc_command[@]}"

  expanded call: /export01/local/fsl/bin/eddy_quad /local_raid/data/HCPD/HCPpipelines-master/testdata/HCD0042420_V1_MR/Diffusion/eddy/eddy_unwarped_images -idx /local_raid/data/HCPD/HCPpipelines-master/testdata/HCD0042420_V1_MR/Diffusion/eddy/index.txt -par /local_raid/data/HCPD/HCPpipelines-master/testdata/HCD0042420_V1_MR/Diffusion/eddy/acqparams.txt -m /local_raid/data/HCPD/HCPpipelines-master/testdata/HCD0042420_V1_MR/Diffusion/eddy/nodif_brain_mask.nii.gz -b /local_raid/data/HCPD/HCPpipelines-master/testdata/HCD0042420_V1_MR/Diffusion/eddy/Pos_Neg.bvals -g /local_raid/data/HCPD/HCPpipelines-master/testdata/HCD0042420_V1_MR/Diffusion/eddy/eddy_unwarped_images.eddy_rotated_bvecs -o /local_raid/data/HCPD/HCPpipelines-master/testdata/HCD0042420_V1_MR/Diffusion/QC -f /local_raid/data/HCPD/HCPpipelines-master/testdata/HCD0042420_V1_MR/Diffusion/topup/topup_Pos_Neg_b0_field.nii.gz -v

      exit code: 1

---------------------------------------------------

===> Aborting execution!

Would anyone possibly have clues to the cause or solution of this error? 

Looking into quad.py (line 63), it looks like the eddyBase file should be an ".nii" or ".nii.gz" file. However, in the expanded call it seems that the eddyBase file name is "eddy_unwarped_images". Could this possibly be the error? 

Thank you for your help, 

Best, 

Shirley 

[Glasser, Matthew]

I bet eddy did not finish correctly and there is an earlier error.  We are actively running this preprocessing now for the “official” data, but getting the data released on NDA is a process…

 

Matt.

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[Wenlan Zhang]

Hi Matt, 

That makes sense- it could be something to do with eddy_openmp, which is taking a very long time (>12 hours). 

I'm also going back and double checking my input parameters. Would you happen to know what echo spacing value is being used the preprocess the official HCP-D data? My echo spacing value currently is 0.689998. 

Thanks, 

Shirley 

[Glasser, Matthew]

The scanner protocol PDF I have says 0.69ms.

[Harms, Michael]

 

Just as an FYI, we’ve worked with Jesper to develop to what we consider an optimal set of parameters for processing this data through ‘eddy’.

 

Cheers,

-MH

 

 

-- 

Michael Harms, Ph.D.

-----------------------------------------------------------

Associate Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.                        Tel: 314-747-6173

St. Louis, MO  63110                          Email: mha...@wustl.edu

 

From: "Glasser, Matthew" <glas...@wustl.edu>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Thursday, July 8, 2021 at 7:33 PM
To: Wenlan Zhang <wenlan.zh...@gmail.com>, HCP-Users <hcp-...@humanconnectome.org>
Subject: Re: [hcp-users] HCPpipelines eddy_postproc.sh Error

 

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