[QUESTION] Freesurfer terminal_output

[mgclark]

I would like to silence the terminal output of interfaces/freesurfer/preprocess ReconAll -- is this possible? Setting ReconAll().inputs.terminal_output was not effective (and does not appear to be in the input spec for ReconAll?) Do I set terminal_output elsewhere? Should I add terminal_output to ReconAllInputSpec?

Potentially relevant PR: #1070

[satra]

@mgclark - ReconAll is derived from CommandLine and therefore should inherit all the inputs including terminal output, as noted in the online documentation or if you do ReconAll.help().

this didn't show me any output in the terminal:

from nipype.interfaces.freesurfer import ReconAll
ra = ReconAll()
ra.inputs.T1_files = '/software/data/studyforrest-data-structural/sub-01/anat/sub-01_T1w.nii.gz'
ra.inputs.subjects_dir = '/tmp/test_fs'
ra.inputs.terminal_output = 'file'
ra.run()

[mgclark]

Aha -- my error was using os.system(ra.cmdline) (instead of ra.run()) to execute the process. The os.system() method does not benefit from the terminal_output functionality. Thanks for the help @satra!