"command 'bet' could not be found on host" 在 Windows 10 通过 Python 3.5 在 FSL 中使用 BET 时出错

Question

我需要对 .nii 图像执行大脑提取。我在 Windows 10 上使用 Anaconda，并且有一个基于 Python 3.5.4 的环境。在 Nipype 上，我从 FSL 找到了 BET，我遵循了代码：

mybet = fsl.BET()
mybet.inputs.in_file = 'example.nii'
mybet.inputs.out_file = 'example_bet.nii' 
result = mybet.run()

请注意，我希望输出文件 example_bet.nii 由 fsl.BET 创建，而不是要覆盖的图像。我只能找到基于 Unix 系统的解决方案，而且似乎需要在基于 Unix 的 OS 上安装 FSL，如果 Windows 中没有虚拟机，这是不可能的。嗯，这是我得到的输出：

171122-12:02:48,988 interface WARNING:
     FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI

---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
<ipython-input-12-5b900fbd5263> in <module>()
      2 mybet.inputs.in_file = 'prova.nii'
      3 mybet.inputs.out_file = 'prova_bet.nii'
----> 4 result = mybet.run()

~\Anaconda3\envs\tensorflow\lib\site-packages\nipype\interfaces\base.py in run(self, **inputs)
   1079                         version=self.version)
   1080         try:
-> 1081             runtime = self._run_wrapper(runtime)
   1082             outputs = self.aggregate_outputs(runtime)
   1083             runtime.endTime = dt.isoformat(dt.utcnow())

~\Anaconda3\envs\tensorflow\lib\site-packages\nipype\interfaces\base.py in _run_wrapper(self, runtime)
   1722 
   1723     def _run_wrapper(self, runtime):
-> 1724         runtime = self._run_interface(runtime)
   1725         return runtime
   1726 

~\Anaconda3\envs\tensorflow\lib\site-packages\nipype\interfaces\fsl\preprocess.py in _run_interface(self, runtime)
    142         # in stderr and if it's set, then update the returncode
    143         # accordingly.
--> 144         runtime = super(BET, self)._run_interface(runtime)
    145         if runtime.stderr:
    146             self.raise_exception(runtime)

~\Anaconda3\envs\tensorflow\lib\site-packages\nipype\interfaces\base.py in _run_interface(self, runtime, correct_return_codes)
   1748         if not exist_val:
   1749             raise IOError("command '%s' could not be found on host %s" %
-> 1750                           (self.cmd.split()[0], runtime.hostname))
   1751         setattr(runtime, 'command_path', cmd_path)
   1752         setattr(runtime, 'dependencies', get_dependencies(executable_name,

OSError: command 'bet' could not be found on host DESKTOP-MYPC
Interface BET failed to run.

我需要切换到 Linux 还是有解决办法？

Answer 1

您只能通过 Docker, Virtual Machine, or Windows Subsystem for Linux 在 Windows 上使用 FSL。运行天真地不可能。

"command 'bet' could not be found on host" 在 Windows 10 通过 Python 3.5 在 FSL 中使用 BET 时出错

"command 'bet' could not be found on host" error while using BET in FSL on Windows 10 via Python 3.5

python

windows

image-processing

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nipype