I will send some PRs to improve/fix fsl cuda-capable tools with the new gpu support.
This one is about eddy:
eddy_openmp is an old command, new fls uses eddy_cpu
eddy_cuda is missing in some version, in those cases if user requests cuda, just use eddy

eddy_cpu does not enable multithread with OMP_NUM_THREADS variable but with --nthr argument

Codecov Report

Attention: coverage is 44.44444% with 5 lines in your changes missing coverage. Please review.

Project coverage is 69.13%. Comparing base (2f85d92) to head (9348f49).

Files with missing lines	%	Lines
nipype/interfaces/fsl/epi.py	44.44%	5 Missing⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           master    #3721       +/-   ##
===========================================
+ Coverage    2.88%   69.13%   +66.24%     
===========================================
  Files        1279     1278        -1     
  Lines       59413    59271      -142     
===========================================
+ Hits         1717    40978    +39261     
+ Misses      57696    18293    -39403     

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the second commit fix this:
EddyInputError: The version compiled for GPU can only use 1 CPU thread (i.e. --nthr=1)