Problems with preprocessing of DWI subject

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1

Hi everyone. I’ve been preprocessing a DWI subjects recently, and I’ve come across this kind of errors:

dwifslpreproc: [ERROR] eddy* --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --topup=field --slm=linear --out=dwi_post_eddy --verbose (app.py:196)
dwifslpreproc: [ERROR] Information from failed command:
dwifslpreproc:
               =========
               eddy_cuda
               =========
               
               
               ===========
               eddy_openmp
               ===========
               eddy: msg=--bvecs should contain a 3xN or Nx3 matrix where N is the number of volumes in --imain
               eddy: msg=Error when attempting to read --bvecs file
               
               
               =========
               eddy_cuda
               =========
               eddy_cuda: error while loading shared libraries: libcudart.so.7.5: cannot open shared object file: No such file or directory
               
               
               ===========
               eddy_openmp
               ===========
               terminate called after throwing an instance of 'EDDY::EddyException'
                 what():  eddy: msg=Error when attempting to read --bvecs file

I’ve been changing the bvals and bvecs, I’ve been checking the DICOM and the DWI to assert whether the header was correct, and I am not able to get the problem of the analysis.

The dirstat is this:

results/Suj_X.nii.gz.mif (b=0) [ 2 directions ]

  Bipolar electrostatic repulsion model:
    nearest-neighbour angles: mean = 90, range [ 90 - 90 ]
    energy: total = inf, mean = inf, range [ 1.79769e+308 - inf ]

  Unipolar electrostatic repulsion model:
    nearest-neighbour angles: mean = 90, range [ 90 - 90 ]
    energy: total = inf, mean = inf, range [ 1.79769e+308 - inf ]

  Spherical Harmonic fit:
    condition numbers for lmax = 2 -> 0: [ ]

  Asymmetry of sampling:
    norm of mean direction vector = 0

The mrinfo -dwgrad of the Suj_X is this:

mrinfo results/Suj_X.nii.gz.mif -dwgrad
0 0 0 0
0 0 0 0

Does someone know what is going on, and how to solve this problem?

Cheers!

1 Like
2

Your data only contains 2 b=0 volumes? No actual diffusion-weighted data at all? That doesn’t sound right… And certainly isn’t something that dwifslpreproc or eddy would expect!

Are you sure you’re feeding in the correct dataset? These may correspond to the reversed phase-encoded scans that are often acquired for distortion correction. Hopefully there is some other (much larger) scan with actual diffusion-weighted data in it…?

3

Thanks for the response!

Yeah, I’ve talked to the technician that took the DWI image, and we are trying to ascertain what could have happened in the trial. Probably something about the adquisition of the image. Hopefuly where are some backups of the adquisition.