Hi all,
I have been trying to run recon-all using ReconAll from nipype.interfaces.freesurfer but getting an error that recon-all can’t be found. I can run it just fine from terminal, however. I am on Ubuntu 18.04 running nipype 1.1.3 and Freesurfer 6.0.0. How do I tell nipype where to find Freesurfer?
File “/home/lars/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/core.py”, line 522, in run
runtime = self._run_interface(runtime)
File “/home/lars/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/core.py”, line 1029, in _run_interface
runtime.hostname))
OSError: No command “recon-all” found on host lars-GE63-7RD. Please check that the corresponding package is installed.
I’m using this schema:
from nipype.interfaces.freesurfer import ReconAll
reconall = ReconAll()
reconall.inputs.subject_id = ‘foo’
reconall.inputs.directive = ‘all’
reconall.inputs.subjects_dir = ‘.’
reconall.inputs.T1_files = ‘structural.nii’
reconall.run()