Defacing tool problem

[Freeklinders]

Hi Marcel,

Sorry for a (perhaps simple) question again, but I am a beginner to MRI analyses. I hope I do not bother you too much. I am trying to deface the T1 scans to share with another site, though I keep receiving the following error when running the command: deface BIDS/ 'anat/*_T1w*'

Traceback (most recent call last):
  File "/data/fjlinders/anaconda3/envs/freek/bin/deface", line 5, in <module>
    from bidscoin.deface import main
  File "/data/fjlinders/anaconda3/envs/freek/lib/python3.6/site-packages/bidscoin/deface.py", line 15, in <module>
    import drmaa
  File "/data/fjlinders/anaconda3/envs/freek/lib/python3.6/site-packages/drmaa/__init__.py", line 65, in <module>
    from .session import JobInfo, JobTemplate, Session
  File "/data/fjlinders/anaconda3/envs/freek/lib/python3.6/site-packages/drmaa/session.py", line 39, in <module>
    from drmaa.helpers import (adapt_rusage, Attribute, attribute_names_iterator,
  File "/data/fjlinders/anaconda3/envs/freek/lib/python3.6/site-packages/drmaa/helpers.py", line 36, in <module>
    from drmaa.wrappers import (drmaa_attr_names_t, drmaa_attr_values_t,
  File "/data/fjlinders/anaconda3/envs/freek/lib/python3.6/site-packages/drmaa/wrappers.py", line 56, in <module>
    _lib = CDLL(libpath, mode=RTLD_GLOBAL)
  File "/data/fjlinders/anaconda3/envs/freek/lib/python3.6/ctypes/__init__.py", line 348, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: /data/fjlinders/anaconda3/envs/freek/lib/python3.6/site-packages/drmaa/: cannot read file data: Is a directory

I first received an error about that I had to define my DRMAA_LIBRARY_PATH, which I did with the command:

export DRMAA_LIBRARY_PATH=/data/fjlinders/anaconda3/envs/freek/lib/python3.6/site-packages/drmaa/
As it looks that my drmaa library is in there. All the other bidscoin functionalities work.

[marcelzwiers]

Hi Freek,

No problem, that is indeed a bug that I fixed some time ago. The fix will become available in the upcoming release, in the meantime you can try it by upgrading to the development version (which is very stable already):

pip install --force-reinstall --no-deps git+https://github.com/Donders-Institute/bidscoin

[Freeklinders]

Thanks a lot, it worked!