Zero-filled volumes after applytopup within dwifslpreproc

1

Hello, I’m currently experiencing the same issue. After troubleshooting, I discovered that when executing the following command with dwifslpreproc, all output file values are set to zero.

Command:  applytopup --imain=applytopup_in_pe1.nii --datain=applytopup_config.txt --inindex=1 --topup=field --out=applytopup_in_pe1_applytopup.nii --method=jac

By using mrstats applytopup_in_pe1_applytopup.nii.gz, it was discovered that

mrstats: [100%] uncompressing image "applytopup_in_pe1_applytopup.nii.gz"
      volume       mean     median        std        min        max      count
       [ 0 ]          0          0          0          0          0    1277952
       [ 1 ]          0          0          0          0          0    1277952
       [ 2 ]          0          0          0          0          0    1277952
       [ 3 ]          0          0          0          0          0    1277952
       [ 4 ]          0          0          0          0          0    1277952
       [ 5 ]          0          0          0          0          0    1277952
       [ 6 ]          0          0          0          0          0    1277952
       [ 7 ]          0          0          0          0          0    1277952
       [ 8 ]          0          0          0          0          0    1277952
......

Would you be able to help resolve this issue? Thank you very much.

2

Hi @hao_xu,

What do the other contents of the the scratch directory look like?

  • Do the input DWIs contain valid image content?
  • Does the FSL topup field estimate look sensible?
    (bear in mind that this provides spline coefficients rather than voxel intensities, so it may not overlap in real space with your image data)
  • What are the contents of the config file?

Rob