element. Please specify either 'title' or 'pagetitle' in the metadata. Falling back to 'CITATION' /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.6/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.6/site-packages/pytest.py' mode='r' encoding='utf-8'> imp.find_module('pytest') /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:121: ResourceWarning: unclosed file <_io.TextIOWrapper name='/projects/adapt_lab/shared/ADS/data/BIDS_data/dataset_description.json' mode='r' encoding='UTF-8'> self.description = json.load(open(target, 'r')) /usr/local/miniconda/lib/python3.6/site-packages/grabbit/core.py:436: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.6/site-packages/bids/layout/config/bids.json' mode='r' encoding='UTF-8'> domain = json.load(open(domain, 'r')) /usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:208: ResourceWarning: unclosed file <_io.TextIOWrapper name='/projects/adapt_lab/shared/ADS/data/BIDS_data/sub-ADS5226/ses-wave2/func/sub-ADS5226_ses-wave2_task-rest_bold.json' mode='r' encoding='utf-8'> encoding='utf-8')) /usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:208: ResourceWarning: unclosed file <_io.TextIOWrapper name='/projects/adapt_lab/shared/ADS/data/BIDS_data/sub-ADS5226/ses-wave2/fmap/sub-ADS5226_ses-wave2_phasediff.json' mode='r' encoding='utf-8'> encoding='utf-8')) /usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:208: ResourceWarning: unclosed file <_io.TextIOWrapper name='/projects/adapt_lab/shared/ADS/data/BIDS_data/sub-ADS5226/ses-wave3/fmap/sub-ADS5226_ses-wave3_phasediff.json' mode='r' encoding='utf-8'> encoding='utf-8')) /usr/local/miniconda/lib/python3.6/site-packages/nipype/workflows/dmri/mrtrix/group_connectivity.py:16: UserWarning: cmp not installed warnings.warn('cmp not installed') /usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py:1887: UserWarning: This has not been fully tested. Please report any failures. warn('This has not been fully tested. Please report any failures.') /usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:208: ResourceWarning: unclosed file <_io.TextIOWrapper name='/projects/adapt_lab/shared/ADS/data/BIDS_data/sub-ADS5226/ses-wave3/func/sub-ADS5226_ses-wave3_task-rest_bold.json' mode='r' encoding='utf-8'> encoding='utf-8')) /usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py:1887: UserWarning: This has not been fully tested. Please report any failures. warn('This has not been fully tested. Please report any failures.') Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ Captured warning (<class 'ResourceWarning'>): unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.6/site-packages/pytest.py' mode='r' encoding='utf-8'> Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.6/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.6/site-packages/pytest.py' mode='r' encoding='utf-8'> imp.find_module('pytest') /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) Captured warning (<class 'PendingDeprecationWarning'>): the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.

[WARNING] This document format requires a nonempty element. Please specify either 'title' or 'pagetitle' in the metadata. Falling back to 'CITATION' /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.6/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.6/site-packages/pytest.py' mode='r' encoding='utf-8'> imp.find_module('pytest') /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:121: ResourceWarning: unclosed file <_io.TextIOWrapper name='/projects/adapt_lab/shared/ADS/data/BIDS_data/dataset_description.json' mode='r' encoding='UTF-8'> self.description = json.load(open(target, 'r')) /usr/local/miniconda/lib/python3.6/site-packages/grabbit/core.py:436: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.6/site-packages/bids/layout/config/bids.json' mode='r' encoding='UTF-8'> domain = json.load(open(domain, 'r')) /usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:208: ResourceWarning: unclosed file <_io.TextIOWrapper name='/projects/adapt_lab/shared/ADS/data/BIDS_data/sub-ADS5226/ses-wave2/func/sub-ADS5226_ses-wave2_task-rest_bold.json' mode='r' encoding='utf-8'> encoding='utf-8')) /usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:208: ResourceWarning: unclosed file <_io.TextIOWrapper name='/projects/adapt_lab/shared/ADS/data/BIDS_data/sub-ADS5226/ses-wave2/fmap/sub-ADS5226_ses-wave2_phasediff.json' mode='r' encoding='utf-8'> encoding='utf-8')) /usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:208: ResourceWarning: unclosed file <_io.TextIOWrapper name='/projects/adapt_lab/shared/ADS/data/BIDS_data/sub-ADS5226/ses-wave3/fmap/sub-ADS5226_ses-wave3_phasediff.json' mode='r' encoding='utf-8'> encoding='utf-8')) /usr/local/miniconda/lib/python3.6/site-packages/nipype/workflows/dmri/mrtrix/group_connectivity.py:16: UserWarning: cmp not installed warnings.warn('cmp not installed') /usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py:1887: UserWarning: This has not been fully tested. Please report any failures. warn('This has not been fully tested. Please report any failures.') /usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:208: ResourceWarning: unclosed file <_io.TextIOWrapper name='/projects/adapt_lab/shared/ADS/data/BIDS_data/sub-ADS5226/ses-wave3/func/sub-ADS5226_ses-wave3_task-rest_bold.json' mode='r' encoding='utf-8'> encoding='utf-8')) /usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py:1887: UserWarning: This has not been fully tested. Please report any failures. warn('This has not been fully tested. Please report any failures.') Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ Captured warning (<class 'ResourceWarning'>): unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.6/site-packages/pytest.py' mode='r' encoding='utf-8'> Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.6/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.6/site-packages/pytest.py' mode='r' encoding='utf-8'> imp.find_module('pytest') /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) Captured warning (<class 'PendingDeprecationWarning'>): the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.