I need to perform brain extraction on .nii images. I am using Anaconda on Windows 10 and have an environment based on Python 3.5.4. On Nipype I found the BET from FSL and I followed the code:
mybet = fsl.BET()
mybet.inputs.in_file = 'example.nii'
mybet.inputs.out_file = 'example_bet.nii'
result = mybet.run()
Please note that I expect the output file example_bet.nii to be created by fsl.BET, not to be an image to be overwritten.
I can only find solutions based on Unix systems and it seems one needs to have FSL installed on a Unix-based OS, which is not possible without a Virtual Machine in Windows.
Well, this is the output I get:
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.
Do I need to switch to Linux or is there a way around it?
You can only use FSL on Windows via Docker, Virtual Machine, or Windows Subsystem for Linux. Running it naively is not possible.