TypeError: environment can only contain strings

[ggsf13]

Summary

I'm working on an image processing task with nipype, and I got the following problem

Actual behavior

Expected behavior

How to replicate the behavior

Script/Workflow details

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "D:\study\project\3D cnn\3DUnetCNN-master\brats\preprocess.py", line 155, in convert_brats_data
    no_bias_correction_modalities=no_bias_correction_modalities)
  File "D:\study\project\3D cnn\3DUnetCNN-master\brats\preprocess.py", line 124, in convert_brats_folder
    normalize_image(image_file, out_file, bias_correction=perform_bias_correction)
  File "D:\study\project\3D cnn\3DUnetCNN-master\brats\preprocess.py", line 112, in normalize_image
    correct_bias(in_file, out_file)
  File "D:\study\project\3D cnn\3DUnetCNN-master\brats\preprocess.py", line 70, in correct_bias
    done = correct.run()
  File "D:\softwares\Annoconda3\lib\site-packages\nipype\interfaces\base\core.py", line 498, in run
    version=self.version)
  File "D:\softwares\Annoconda3\lib\site-packages\nipype\interfaces\ants\base.py", line 125, in version
    return Info.version()
  File "D:\softwares\Annoconda3\lib\site-packages\nipype\interfaces\base\core.py", line 1283, in version
    terminal_output='allatonce').run()
  File "D:\softwares\Annoconda3\lib\site-packages\nipype\interfaces\base\core.py", line 516, in run
    runtime = self._run_interface(runtime)
  File "D:\softwares\Annoconda3\lib\site-packages\nipype\interfaces\base\core.py", line 1020, in _run_interface
    runtime = run_command(runtime, output=self.terminal_output)
  File "D:\softwares\Annoconda3\lib\site-packages\nipype\interfaces\base\core.py", line 750, in run_command
    close_fds=False,
  File "D:\softwares\Annoconda3\lib\subprocess.py", line 709, in __init__
    restore_signals, start_new_session)
  File "D:\softwares\Annoconda3\lib\subprocess.py", line 997, in _execute_child
    startupinfo)
TypeError: environment can only contain strings

here are the codes that produced the error:

        def _execute_child(self, args, executable, preexec_fn, close_fds,
                           pass_fds, cwd, env,
                           startupinfo, creationflags, shell,
                           p2cread, p2cwrite,
                           c2pread, c2pwrite,
                           errread, errwrite,
                           unused_restore_signals, unused_start_new_session):
            """Execute program (MS Windows version)"""

            assert not pass_fds, "pass_fds not supported on Windows."

            if not isinstance(args, str):
                args = list2cmdline(args)

            # Process startup details
            if startupinfo is None:
                startupinfo = STARTUPINFO()
            if -1 not in (p2cread, c2pwrite, errwrite):
                startupinfo.dwFlags |= _winapi.STARTF_USESTDHANDLES
                startupinfo.hStdInput = p2cread
                startupinfo.hStdOutput = c2pwrite
                startupinfo.hStdError = errwrite

            if shell:
                startupinfo.dwFlags |= _winapi.STARTF_USESHOWWINDOW
                startupinfo.wShowWindow = _winapi.SW_HIDE
                comspec = os.environ.get("COMSPEC", "cmd.exe")
                args = '{} /c "{}"'.format (comspec, args)

            # Start the process
            try:
                hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
                                         # no special security
                                         None, None,
                                         int(not close_fds),
                                         creationflags,
                                         env,
                                         os.fspath(cwd) if cwd is not None else None,
                                         startupinfo)

Platform details:

{'pkg_path': 'D:\\softwares\\Annoconda3\\lib\\site-packages\\nipype',
 'commit_source': 'installation',
 'commit_hash': 'bded0d02',
 'nipype_version': '1.0.1',
 'sys_version': '3.6.3 |Anaconda custom (64-bit)| (default, Oct 15 2017, 03:27:45) [MSC v.1900 64 bit (AMD64)]',
 'sys_executable': 'D:\\softwares\\Annoconda3\\python.exe',
 'sys_platform': 'win32',
 'numpy_version': '1.13.3',
 'scipy_version': '0.19.1',
 'networkx_version': '2.0',
 'nibabel_version': '2.2.1',
 'traits_version': '4.6.0'}
1.0.1

Execution environment

can anyone help me with this? any suggestion is appreciated.

[effigies]

So it looks like this may be an incompatibility of 3DUnetCNN with more recent versions of nipype. Do they provide docker images that pre-package known compatible versions? If not, this may be worth tracking down on their side, and then seeing if there's something we can do here to resolve the issue.

[glioi]

I have exactly the same issue! Can anyone help with this?

[yunfeiluo]

I also have the same issue when using SPM interface. Is there any solutions? I'm using win10, and have spm running correctly in matlab.

[effigies]

Can you share the code producing the issue?

[yunfeiluo]

I think maybe this is the issue with popen under win10 environment. There are no such error when I switch to run my code in docker.

[AugustKRZhu]

Hi, I also face this problem when I just used the example code.

from nipype.interfaces.dcm2nii import Dcm2niix

converter = Dcm2niix()
converter.inputs.source_dir = 'xxx'
converter.inputs.compression = 5
converter.inputs.output_dir = 'yyy'
converter.cmdline
'dcm2niix -b y -z y -5 -x n -t n -m n -o ds005 -s n -v n dicomdir'
converter.run()

can anybody solve this?

Thanks

[effigies]

It looks like there are some related but not identical issues. The original issue is just a too-old nipype. That bug was fixed in #2085.

This latest is unclear exactly why it's happening, since it's occurring in version_from_command, which should be unused. Submitting a patch to fix it until we can remove it entirely.

[effigies]

Oh, actually, it seems to be the opposite. Windows has gone from only permitting bytes to only permitting strings.

[effigies]

Can people try installing my branch into your environment and testing?

pip install git+https://github.com/effigies/nipype.git@fix/canonicalize_env

[effigies]

Anybody up for a test? I don't have a Windows machine to test on.