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OSError：在主机 pc 上找不到命令“N4BiasFieldCorrection”。请检查是否安装了相应的软件包。

我在使用 nipype 时遇到问题。你能帮忙吗？

from nipype.interfaces.ants import N4BiasFieldCorrection

n4 = N4BiasFieldCorrection()

n4.inputs.dimension = 3

n4.inputs.input_image =('/home/abhayadev/Desktop/project/Dataset/BRATS2013_CHALLENGE/Challenge/HG/0301/VSD.Brain.XX.O.MR_Flair/VSD.Brain.XX.O.MR_Flair.17572.mha')

n4.inputs.n_iterations = [20, 20, 10, 5]

n4.run()

res=n4.run()

print(res)

输出 ：

``OSError                                   Traceback (most recent call last)
<ipython-input-10-49ae4ec58583> in <module>
5 n4.inputs.input_image =`enter code here`('/home/abhayadev/Desktop/project/Dataset/BRATS2013_CHALLENGE/Challenge/HG/0301/VSD.Brain.XX.O.MR_Flair/VSD.Brain.XX.O.MR_Flair.17572.mha')
      6 n4.inputs.n_iterations = [20, 20, 10, 5]
----> 7 n4.run()
      8 res=n4.run()
      9 print(res)

~/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py in run(self, cwd, ignore_exception, **inputs)
    374         try:
    375             runtime = self._pre_run_hook(runtime)
--> 376             runtime = self._run_interface(runtime)
    377             runtime = self._post_run_hook(runtime)
    378             outputs = self.aggregate_outputs(runtime)

~/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py in _run_interface(self, runtime, correct_return_codes)
    750                 'No command "%s" found on host %s. Please check that the '
    751                 'corresponding package is installed.' % (executable_name,
--> 752                                                          runtime.hostname))
    753 
    754         runtime.command_path = cmd_path

OSError: No command "N4BiasFieldCorrection" found on host abhayadev. Please check that the corresponding package is installed.
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1 回答 1

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您需要在 PATH 变量中包含 ANTS 的安装目录。从安装指南：

假设您的安装前缀是 /opt/ANTs，现在将有一个二进制目录 /opt/ANTs/bin，其中包含 ANTs 可执行文件和脚本。这些脚本还需要 ANTSPATH 指向包含尾部斜杠的 bin 目录。

对于 bash shell（Mac 和某些 Linux 上的默认设置），您需要设置

export ANTSPATH=/opt/ANTs/bin/
export PATH=${ANTSPATH}:$PATH

如果您在 neurodocker 中使用 nipype（推荐），您必须： source activate neuro让 ANTS 命令可用。

于 2020-03-06T08:54:58.707 回答