Hi,
I’ve been running fmriprep through docker just fine so far, but need to do it on an external HDD. It has read and write access enabled on my iOS. however, when running fmriprep through docker wrapper I get the following message. Can somebody please suggest a solution? Thank you!
fmriprep-docker /Volumes/volumename/test /Volumes/volumename/test/derivatives participant --participant-label 1006 --fs-license-file /Volumes/volumename/license.txt --verbose --stop-on-first-crash --w /Volumes/volumename/temp
Traceback (most recent call last):File “/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/base.py”, line 1276, in _execute_context
self.dialect.do_execute(
File “/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/default.py”, line 608, in do_execute
cursor.execute(statement, parameters)
sqlite3.OperationalError: attempt to write a readonly databaseThe above exception was the direct cause of the following exception:
Traceback (most recent call last):
File “/opt/conda/bin/fmriprep”, line 8, in
sys.exit(main())
File “/opt/conda/lib/python3.8/site-packages/fmriprep/cli/run.py”, line 38, in main
parse_args()
File “/opt/conda/lib/python3.8/site-packages/fmriprep/cli/parser.py”, line 668, in parse_args
config.from_dict(vars(opts))
File “/opt/conda/lib/python3.8/site-packages/fmriprep/config.py”, line 664, in from_dict
execution.load(settings)
File “/opt/conda/lib/python3.8/site-packages/fmriprep/config.py”, line 238, in load
cls.init()
File “/opt/conda/lib/python3.8/site-packages/fmriprep/config.py”, line 481, in init
cls._layout = BIDSLayout(
File “/opt/conda/lib/python3.8/site-packages/bids/layout/layout.py”, line 140, in init
self.connection_manager = ConnectionManager(
File “/opt/conda/lib/python3.8/site-packages/bids/layout/db.py”, line 45, in init
self.reset_database(init_args, config)
File “/opt/conda/lib/python3.8/site-packages/bids/layout/db.py”, line 104, in reset_database
Base.metadata.create_all(self.engine)
File “/opt/conda/lib/python3.8/site-packages/sqlalchemy/sql/schema.py”, line 4664, in create_all
bind._run_visitor(
File “/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/base.py”, line 2095, in _run_visitor
conn._run_visitor(visitorcallable, element, **kwargs)
File “/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/base.py”, line 1656, in _run_visitor
visitorcallable(self.dialect, self, **kwargs).traverse_single(element)
File “/opt/conda/lib/python3.8/site-packages/sqlalchemy/sql/visitors.py”, line 145, in traverse_single
return meth(obj, **kw)
File “/opt/conda/lib/python3.8/site-packages/sqlalchemy/sql/ddl.py”, line 783, in visit_metadata
self.traverse_single(
File “/opt/conda/lib/python3.8/site-packages/sqlalchemy/sql/visitors.py”, line 145, in traverse_single
return meth(obj, **kw)
File “/opt/conda/lib/python3.8/site-packages/sqlalchemy/sql/ddl.py”, line 827, in visit_table
self.connection.execute(
File “/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/base.py”, line 1011, in execute
return meth(self, multiparams, params)
File “/opt/conda/lib/python3.8/site-packages/sqlalchemy/sql/ddl.py”, line 72, in _execute_on_connection
return connection._execute_ddl(self, multiparams, params)
File “/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/base.py”, line 1068, in _execute_ddl
ret = self._execute_context(
File “/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/base.py”, line 1316, in _execute_context
self.handle_dbapi_exception(
File “/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/base.py”, line 1510, in handle_dbapi_exception
util.raise(
File “/opt/conda/lib/python3.8/site-packages/sqlalchemy/util/compat.py”, line 182, in raise
raise exception
File “/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/base.py”, line 1276, in _execute_context
self.dialect.do_execute(
File “/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/default.py”, line 608, in do_execute
cursor.execute(statement, parameters)
sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) attempt to write a readonly database
[SQL:
CREATE TABLE configs (
name VARCHAR NOT NULL,
_default_path_patterns VARCHAR,
PRIMARY KEY (name)
)]
(Background on this error at: http://sqlalche.me/e/13/e3q8)
fMRIPrep: Please report errors to https://github.com/nipreps/fmriprep/issues