I’m receiving this error when I try out pydeface on my T1 data. It looks like the error is fsl related, but I’m not sure what the issue is. I’ve installed nipype nibabel and fsl
Defacing…
/Users/me/Documents/lab/bids/attempt1/sub-S03520180905/ses-18444/anat/sub-S03520180905_ses-18444_T1w.nii.gz
181115-13:50:58,113 nipype.interface INFO:
stderr 2018-11-15T13:50:58.113232:Unrecognised option l
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", line 174, in _run_module_as_main
"main", fname, loader, pkg_name)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/Users/me/pydeface/pydeface/main.py", line 154, in <module>
main()
File "/Users/me/pydeface/pydeface/main.py", line 105, in main
flirt.run()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 522, in run
runtime = self._run_interface(runtime)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 1038, in _run_interface
self.raise_exception(runtime)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 975, in raise_exception
).format(**runtime.dictcopy()))
RuntimeError: Command:
flirt -in /Users/me/Library/Caches/Python-Eggs/pydeface-2.0-py2.7.egg-tmp/pydeface/data/mean_reg2mean.nii.gz -ref /Users/me/Documents/lab/bids/attempt1/sub-S03520180905/ses-18444/anat/sub-S03520180905_ses-18444_T1w.nii.gz -out /var/folders/7g/7c4hf0c51xz4m0x4j17z4bc80000gp/T/tmplQyBjy -omat /var/folders/7g/7c4hf0c51xz4m0x4j17z4bc80000gp/T/tmpvp4fG9.mat -searchcost mutualinfo
Standard output:
Standard error:
Unrecognised option l
Return code: 255