Error using fsl.EDDY

[DavidBarriere]

Summary

EDDY current and motion correction of dw data.

Actual behavior

Expected behavior

How to replicate the behavior

Script/Workflow details

eddy = fsl.Eddy(in_file = 'dwi_denoised.nii.gz',
                in_mask  = 'dw_01_mask.nii.gz',
                in_index = 'index.txt',
                in_acqp  = 'topup_parameters_dw.txt',
                in_topup_fieldcoef = "TopUp_results_fieldcoef.nii.gz",
                in_topup_movpar = 'TopUp_results_movpar.txt',
                in_bvec  = 'dw_01.bvec',
                in_bval  = 'dw_01.bval')
eddy.run()

Platform details:

230621-11:14:36,530 nipype.interface INFO:
	 stdout 2023-06-21T11:14:36.530774:
---------------------------------------------------------------------------
UnicodeDecodeError                        Traceback (most recent call last)
Input In [70], in <cell line: 13>()
      2 os.chdir(data_path)
      5 eddy = fsl.Eddy(in_file = 'dwi_denoised.nii.gz',
      6                 in_mask  = 'dw_01_mask.nii.gz',
      7                 in_index = 'index_6.txt',
   (...)
     11                 in_bvec  = 'dw_01.bvec',
     12                 in_bval  = 'dw_01.bval')
---> 13 eddy.run()
     15 print('Elapsed time:',timeit.timeit())

File ~/.local/lib/python3.8/site-packages/nipype/interfaces/base/core.py:398, in BaseInterface.run(self, cwd, ignore_exception, **inputs)
    396 # Run interface
    397 runtime = self._pre_run_hook(runtime)
--> 398 runtime = self._run_interface(runtime)
    399 runtime = self._post_run_hook(runtime)
    400 # Collect outputs

File ~/.local/lib/python3.8/site-packages/nipype/interfaces/fsl/epi.py:993, in Eddy._run_interface(self, runtime)
    985 if all(
    986     (
    987         FSLDIR != "",
   (...)
    990     )
    991 ):
    992     self._cmd = "eddy"
--> 993 runtime = super(Eddy, self)._run_interface(runtime)
    995 # Restore command to avoid side-effects
    996 self._cmd = cmd

File ~/.local/lib/python3.8/site-packages/nipype/interfaces/base/core.py:765, in CommandLine._run_interface(self, runtime, correct_return_codes)
    759 runtime.command_path = cmd_path
    760 runtime.dependencies = (
    761     get_dependencies(executable_name, runtime.environ)
    762     if self._ldd
    763     else "<skipped>"
    764 )
--> 765 runtime = run_command(
    766     runtime,
    767     output=self.terminal_output,
    768     write_cmdline=self.write_cmdline,
    769 )
    770 return runtime

File ~/.local/lib/python3.8/site-packages/nipype/utils/subprocess.py:141, in run_command(runtime, output, timeout, write_cmdline)
    139 while proc.returncode is None:
    140     proc.poll()
--> 141     _process()
    143 _process(drain=1)
    145 # collect results, merge and return

File ~/.local/lib/python3.8/site-packages/nipype/utils/subprocess.py:137, in run_command.<locals>._process(drain)
    135 else:
    136     for stream in res[0]:
--> 137         stream.read(drain)

File ~/.local/lib/python3.8/site-packages/nipype/utils/subprocess.py:42, in Stream.read(self, drain)
     40 def read(self, drain=0):
     41     "Read from the file descriptor. If 'drain' set, read until EOF."
---> 42     while self._read(drain) is not None:
     43         if not drain:
     44             break

File ~/.local/lib/python3.8/site-packages/nipype/utils/subprocess.py:49, in Stream._read(self, drain)
     47 "Read from the file descriptor"
     48 fd = self.fileno()
---> 49 buf = os.read(fd, 4096).decode(self.default_encoding)
     50 if not buf and not self._buf:
     51     return None

**UnicodeDecodeError: 'utf-8' codec can't decode byte 0xdd in position 1: invalid continuation byte**
-->

Execution environment

Ubuntu 20.04
NIPYPE : 1.8.4
FSL : 6.0.6.5
Python 3.8.10

[DavidBarriere]

Could you please help me to debugg the EDDY function ?

[effigies]

Can you print(eddy.cmdline) and then try running the result yourself, and see what you get?