python problem from nipype.interfaces.ants import N4BiasFieldCorrection

Question

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

i have problem using nipype.can you plese help?

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)

output :

``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.

Answer 1

You need to have ANTS's install directory in your PATH variable. From the install guide:

Assuming your install prefix was /opt/ANTs, there will now be a binary directory /opt/ANTs/bin, containing the ANTs executables and scripts. The scripts additionally require ANTSPATH to point to the bin directory including a trailing slash.

For the bash shell (default on Mac and some Linux), you need to set

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

If you use nipype within neurodocker (would recommend) you have to: source activate neuro to have the ANTS command available.