Welcome: root, 2021-04-10 05:02 DPABISurf: A Surface-Based Resting-State fMRI Data Analysis Toolbox. Release = V1.5_201201 Copyright(c) 2019; GNU GENERAL PUBLIC LICENSE Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Chaoyang District, Beijing 100101, China; Mail to Initiator: YAN Chao-Gan Programmers: YAN Chao-Gan; WANG Xin-Di; LU Bin http://rfmri.org/dpabi ----------------------------------------------------------- Citing Information: DPABISurf is a surface-based resting-state fMRI data analysis toolbox evolved from DPABI/DPARSF, as easy-to-use as DPABI/DPARSF. DPABISurf is based on fMRIPrep 20.2.1 (Esteban et al., 2018) (RRID:SCR_016216), and based on FreeSurfer 6.0.1 (Dale et al., 1999) (RRID:SCR_001847), ANTs 2.3.3 (Avants et al., 2008) (RRID:SCR_004757), FSL 5.0.9 (Jenkinson et al., 2002) (RRID:SCR_002823), AFNI 20160207 (Cox, 1996) (RRID:SCR_005927), SPM12 (Ashburner, 2012) (RRID:SCR_007037), dcm2niix (Li et al., 2016) (RRID:SCR_014099), PALM alpha115 (Winkler et al., 2016), GNU Parallel (Tange, 2011), MATLAB (The MathWorks Inc., Natick, MA, US) (RRID:SCR_001622), Docker (https://docker.com) (RRID:SCR_016445), and DPABI V5.1 (Yan et al., 2016) (RRID:SCR_010501). Chris Rorden's dcm2niiX version v1.0.20201102 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 x86-64 (64-bit Linux) Found 240 DICOM file(s) UINT16->INT16 Future release will change default. github.com/rordenlab/dcm2niix/issues/338 Convert 240 DICOM as /media/DataWork/DemoData/DemoData/DemoRaw/DemoData/FunImg/Sub_001/Sub_001_ge_func_31x31x30_240_RS_20071016110634_4 (64x64x33x240) Conversion required 3.682571 seconds (0.280148 for core code). Converting Functional Images:Sub_001 OKChris Rorden's dcm2niiX version v1.0.20201102 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 x86-64 (64-bit Linux) Found 240 DICOM file(s) UINT16->INT16 Future release will change default. github.com/rordenlab/dcm2niix/issues/338 Convert 240 DICOM as /media/DataWork/DemoData/DemoData/DemoRaw/DemoData/FunImg/Sub_002/Sub_002_ge_func_31x31x30_240_RS_20070929154622_4 (64x64x33x240) Conversion required 4.135905 seconds (0.286009 for core code). Converting Functional Images:Sub_002 OKChris Rorden's dcm2niiX version v1.0.20201102 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 x86-64 (64-bit Linux) Found 240 DICOM file(s) UINT16->INT16 Future release will change default. github.com/rordenlab/dcm2niix/issues/338 Convert 240 DICOM as /media/DataWork/DemoData/DemoData/DemoRaw/DemoData/FunImg/Sub_003/Sub_003_ge_func_31x31x30_240_RS_20070930090506_4 (64x64x33x240) Conversion required 3.766850 seconds (0.283346 for core code). Converting Functional Images:Sub_003 OK Chris Rorden's dcm2niiX version v1.0.20201102 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 x86-64 (64-bit Linux) Found 128 DICOM file(s) UINT16->INT16 Future release will change default. github.com/rordenlab/dcm2niix/issues/338 Convert 128 DICOM as /media/DataWork/DemoData/DemoData/DemoRaw/DemoData/T1Img/Sub_001/Sub_001_t1_mprage_sag_20071016110634_6 (256x256x128x1) Cropping from slice 51 to 220 (of 256) Conversion required 1.542585 seconds (0.165205 for core code). Converting T1 Images:Sub_001 OKChris Rorden's dcm2niiX version v1.0.20201102 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 x86-64 (64-bit Linux) Found 128 DICOM file(s) UINT16->INT16 Future release will change default. github.com/rordenlab/dcm2niix/issues/338 Convert 128 DICOM as /media/DataWork/DemoData/DemoData/DemoRaw/DemoData/T1Img/Sub_002/Sub_002_t1_mprage_sag_20070929154622_7 (256x256x128x1) Cropping from slice 43 to 212 (of 256) Conversion required 1.768023 seconds (0.167754 for core code). Converting T1 Images:Sub_002 OKChris Rorden's dcm2niiX version v1.0.20201102 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 x86-64 (64-bit Linux) Found 128 DICOM file(s) UINT16->INT16 Future release will change default. github.com/rordenlab/dcm2niix/issues/338 Convert 128 DICOM as /media/DataWork/DemoData/DemoData/DemoRaw/DemoData/T1Img/Sub_003/Sub_003_t1_mprage_sag_20070930090506_10 (256x256x128x1) Cropping from slice 47 to 216 (of 256) Conversion required 1.644728 seconds (0.164760 for core code). Converting T1 Images:Sub_003 OK Starting parallel pool (parpool) using the 'local' profile ... connected to 12 workers. Removing First 10 Time Points: Sub_003 OK Removing First 10 Time Points: Sub_002 OK Removing First 10 Time Points: Sub_001 OK Converting DPARSFA to BIDS structure... Parallel pool using the 'local' profile is shutting down. Preprocessing with fmriprep, this process is very time consuming, please be patient... Academic tradition requires you to cite works you base your article on. When using programs that use GNU Parallel to process data for publication please cite: O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, February 2011:42-47. This helps funding further development; AND IT WON'T COST YOU A CENT. If you pay 10000 EUR you should feel free to use GNU Parallel without citing. To silence this citation notice: run 'parallel --citation'. /usr/local/miniconda/lib/python3.7/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the `indexer` argument. warnings.warn("The ability to pass arguments to BIDSLayout that control " Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1277, in _execute_context cursor, statement, parameters, context File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 593, in do_execute cursor.execute(statement, parameters) sqlite3.OperationalError: database is locked The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/usr/local/miniconda/bin/fmriprep", line 10, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 17, in main parse_args() File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/parser.py", line 602, in parse_args config.from_dict(vars(opts)) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 617, in from_dict execution.load(settings) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 218, in load cls.init() File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 453, in init re.compile(r"^\."), File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 151, in __init__ database_path, reset_database, config, init_args) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/db.py", line 48, in __init__ self.reset_database(init_args, config) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/db.py", line 105, in reset_database Base.metadata.create_all(self.engine) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/schema.py", line 4554, in create_all ddl.SchemaGenerator, self, checkfirst=checkfirst, tables=tables File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 2095, in _run_visitor conn._run_visitor(visitorcallable, element, **kwargs) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1656, in _run_visitor visitorcallable(self.dialect, self, **kwargs).traverse_single(element) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/visitors.py", line 145, in traverse_single return meth(obj, **kw) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 787, in visit_metadata _is_metadata_operation=True, File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/visitors.py", line 145, in traverse_single return meth(obj, **kw) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 832, in visit_table include_foreign_key_constraints, # noqa File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1011, in execute return meth(self, multiparams, params) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 72, in _execute_on_connection return connection._execute_ddl(self, multiparams, params) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1073, in _execute_ddl compiled, File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1317, in _execute_context e, statement, parameters, cursor, context File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1511, in _handle_dbapi_exception sqlalchemy_exception, with_traceback=exc_info[2], from_=e File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 182, in raise_ raise exception File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1277, in _execute_context cursor, statement, parameters, context File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 593, in do_execute cursor.execute(statement, parameters) sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) database is locked [SQL: CREATE TABLE layout_info ( root VARCHAR NOT NULL, absolute_paths BOOLEAN, _derivatives VARCHAR, _config VARCHAR, PRIMARY KEY (root), CHECK (absolute_paths IN (0, 1)) ) ] (Background on this error at: http://sqlalche.me/e/13/e3q8) /usr/local/miniconda/lib/python3.7/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the `indexer` argument. warnings.warn("The ability to pass arguments to BIDSLayout that control " Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1277, in _execute_context cursor, statement, parameters, context File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 593, in do_execute cursor.execute(statement, parameters) sqlite3.OperationalError: database is locked The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/usr/local/miniconda/bin/fmriprep", line 10, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 17, in main parse_args() File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/parser.py", line 602, in parse_args config.from_dict(vars(opts)) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 617, in from_dict execution.load(settings) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 218, in load cls.init() File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 453, in init re.compile(r"^\."), File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 151, in __init__ database_path, reset_database, config, init_args) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/db.py", line 48, in __init__ self.reset_database(init_args, config) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/db.py", line 105, in reset_database Base.metadata.create_all(self.engine) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/schema.py", line 4554, in create_all ddl.SchemaGenerator, self, checkfirst=checkfirst, tables=tables File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 2095, in _run_visitor conn._run_visitor(visitorcallable, element, **kwargs) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1656, in _run_visitor visitorcallable(self.dialect, self, **kwargs).traverse_single(element) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/visitors.py", line 145, in traverse_single return meth(obj, **kw) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 787, in visit_metadata _is_metadata_operation=True, File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/visitors.py", line 145, in traverse_single return meth(obj, **kw) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 832, in visit_table include_foreign_key_constraints, # noqa File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1011, in execute return meth(self, multiparams, params) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 72, in _execute_on_connection return connection._execute_ddl(self, multiparams, params) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1073, in _execute_ddl compiled, File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1317, in _execute_context e, statement, parameters, cursor, context File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1511, in _handle_dbapi_exception sqlalchemy_exception, with_traceback=exc_info[2], from_=e File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 182, in raise_ raise exception File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1277, in _execute_context cursor, statement, parameters, context File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 593, in do_execute cursor.execute(statement, parameters) sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) database is locked [SQL: CREATE TABLE layout_info ( root VARCHAR NOT NULL, absolute_paths BOOLEAN, _derivatives VARCHAR, _config VARCHAR, PRIMARY KEY (root), CHECK (absolute_paths IN (0, 1)) ) ] (Background on this error at: http://sqlalche.me/e/13/e3q8) /usr/local/miniconda/lib/python3.7/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the `indexer` argument. warnings.warn("The ability to pass arguments to BIDSLayout that control " Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1277, in _execute_context cursor, statement, parameters, context File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 593, in do_execute cursor.execute(statement, parameters) sqlite3.OperationalError: database is locked The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/usr/local/miniconda/bin/fmriprep", line 10, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 17, in main parse_args() File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/parser.py", line 602, in parse_args config.from_dict(vars(opts)) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 617, in from_dict execution.load(settings) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 218, in load cls.init() File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 453, in init re.compile(r"^\."), File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 151, in __init__ database_path, reset_database, config, init_args) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/db.py", line 48, in __init__ self.reset_database(init_args, config) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/db.py", line 105, in reset_database Base.metadata.create_all(self.engine) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/schema.py", line 4554, in create_all ddl.SchemaGenerator, self, checkfirst=checkfirst, tables=tables File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 2095, in _run_visitor conn._run_visitor(visitorcallable, element, **kwargs) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1656, in _run_visitor visitorcallable(self.dialect, self, **kwargs).traverse_single(element) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/visitors.py", line 145, in traverse_single return meth(obj, **kw) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 787, in visit_metadata _is_metadata_operation=True, File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/visitors.py", line 145, in traverse_single return meth(obj, **kw) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 832, in visit_table include_foreign_key_constraints, # noqa File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1011, in execute return meth(self, multiparams, params) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 72, in _execute_on_connection return connection._execute_ddl(self, multiparams, params) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1073, in _execute_ddl compiled, File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1317, in _execute_context e, statement, parameters, cursor, context File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1511, in _handle_dbapi_exception sqlalchemy_exception, with_traceback=exc_info[2], from_=e File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 182, in raise_ raise exception File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1277, in _execute_context cursor, statement, parameters, context File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 593, in do_execute cursor.execute(statement, parameters) sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) database is locked [SQL: CREATE TABLE layout_info ( root VARCHAR NOT NULL, absolute_paths BOOLEAN, _derivatives VARCHAR, _config VARCHAR, PRIMARY KEY (root), CHECK (absolute_paths IN (0, 1)) ) ] (Background on this error at: http://sqlalche.me/e/13/e3q8) These subjects have not run fmriprep yet: 'sub-Sub001' 'sub-Sub002' 'sub-Sub003' Re-run the failed subjects with fmriprep, this process is very time consuming, please be patient... Academic tradition requires you to cite works you base your article on. When using programs that use GNU Parallel to process data for publication please cite: O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, February 2011:42-47. This helps funding further development; AND IT WON'T COST YOU A CENT. If you pay 10000 EUR you should feel free to use GNU Parallel without citing. To silence this citation notice: run 'parallel --citation'. /usr/local/miniconda/lib/python3.7/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the `indexer` argument. warnings.warn("The ability to pass arguments to BIDSLayout that control " Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1277, in _execute_context cursor, statement, parameters, context File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 593, in do_execute cursor.execute(statement, parameters) sqlite3.OperationalError: database is locked The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/usr/local/miniconda/bin/fmriprep", line 10, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 17, in main parse_args() File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/parser.py", line 602, in parse_args config.from_dict(vars(opts)) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 617, in from_dict execution.load(settings) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 218, in load cls.init() File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 453, in init re.compile(r"^\."), File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 151, in __init__ database_path, reset_database, config, init_args) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/db.py", line 48, in __init__ self.reset_database(init_args, config) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/db.py", line 105, in reset_database Base.metadata.create_all(self.engine) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/schema.py", line 4554, in create_all ddl.SchemaGenerator, self, checkfirst=checkfirst, tables=tables File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 2095, in _run_visitor conn._run_visitor(visitorcallable, element, **kwargs) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1656, in _run_visitor visitorcallable(self.dialect, self, **kwargs).traverse_single(element) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/visitors.py", line 145, in traverse_single return meth(obj, **kw) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 787, in visit_metadata _is_metadata_operation=True, File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/visitors.py", line 145, in traverse_single return meth(obj, **kw) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 832, in visit_table include_foreign_key_constraints, # noqa File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1011, in execute return meth(self, multiparams, params) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 72, in _execute_on_connection return connection._execute_ddl(self, multiparams, params) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1073, in _execute_ddl compiled, File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1317, in _execute_context e, statement, parameters, cursor, context File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1511, in _handle_dbapi_exception sqlalchemy_exception, with_traceback=exc_info[2], from_=e File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 182, in raise_ raise exception File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1277, in _execute_context cursor, statement, parameters, context File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 593, in do_execute cursor.execute(statement, parameters) sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) database is locked [SQL: CREATE TABLE layout_info ( root VARCHAR NOT NULL, absolute_paths BOOLEAN, _derivatives VARCHAR, _config VARCHAR, PRIMARY KEY (root), CHECK (absolute_paths IN (0, 1)) ) ] (Background on this error at: http://sqlalche.me/e/13/e3q8) /usr/local/miniconda/lib/python3.7/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the `indexer` argument. warnings.warn("The ability to pass arguments to BIDSLayout that control " Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1277, in _execute_context cursor, statement, parameters, context File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 593, in do_execute cursor.execute(statement, parameters) sqlite3.OperationalError: database is locked The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/usr/local/miniconda/bin/fmriprep", line 10, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 17, in main parse_args() File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/parser.py", line 602, in parse_args config.from_dict(vars(opts)) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 617, in from_dict execution.load(settings) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 218, in load cls.init() File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 453, in init re.compile(r"^\."), File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 151, in __init__ database_path, reset_database, config, init_args) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/db.py", line 48, in __init__ self.reset_database(init_args, config) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/db.py", line 105, in reset_database Base.metadata.create_all(self.engine) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/schema.py", line 4554, in create_all ddl.SchemaGenerator, self, checkfirst=checkfirst, tables=tables File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 2095, in _run_visitor conn._run_visitor(visitorcallable, element, **kwargs) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1656, in _run_visitor visitorcallable(self.dialect, self, **kwargs).traverse_single(element) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/visitors.py", line 145, in traverse_single return meth(obj, **kw) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 787, in visit_metadata _is_metadata_operation=True, File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/visitors.py", line 145, in traverse_single return meth(obj, **kw) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 832, in visit_table include_foreign_key_constraints, # noqa File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1011, in execute return meth(self, multiparams, params) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 72, in _execute_on_connection return connection._execute_ddl(self, multiparams, params) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1073, in _execute_ddl compiled, File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1317, in _execute_context e, statement, parameters, cursor, context File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1511, in _handle_dbapi_exception sqlalchemy_exception, with_traceback=exc_info[2], from_=e File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 182, in raise_ raise exception File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1277, in _execute_context cursor, statement, parameters, context File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 593, in do_execute cursor.execute(statement, parameters) sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) database is locked [SQL: CREATE TABLE layout_info ( root VARCHAR NOT NULL, absolute_paths BOOLEAN, _derivatives VARCHAR, _config VARCHAR, PRIMARY KEY (root), CHECK (absolute_paths IN (0, 1)) ) ] (Background on this error at: http://sqlalche.me/e/13/e3q8) /usr/local/miniconda/lib/python3.7/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the `indexer` argument. warnings.warn("The ability to pass arguments to BIDSLayout that control " Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1277, in _execute_context cursor, statement, parameters, context File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 593, in do_execute cursor.execute(statement, parameters) sqlite3.OperationalError: database is locked The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/usr/local/miniconda/bin/fmriprep", line 10, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 17, in main parse_args() File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/parser.py", line 602, in parse_args config.from_dict(vars(opts)) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 617, in from_dict execution.load(settings) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 218, in load cls.init() File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 453, in init re.compile(r"^\."), File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 151, in __init__ database_path, reset_database, config, init_args) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/db.py", line 48, in __init__ self.reset_database(init_args, config) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/db.py", line 105, in reset_database Base.metadata.create_all(self.engine) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/schema.py", line 4554, in create_all ddl.SchemaGenerator, self, checkfirst=checkfirst, tables=tables File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 2095, in _run_visitor conn._run_visitor(visitorcallable, element, **kwargs) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1656, in _run_visitor visitorcallable(self.dialect, self, **kwargs).traverse_single(element) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/visitors.py", line 145, in traverse_single return meth(obj, **kw) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 787, in visit_metadata _is_metadata_operation=True, File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/visitors.py", line 145, in traverse_single return meth(obj, **kw) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 832, in visit_table include_foreign_key_constraints, # noqa File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1011, in execute return meth(self, multiparams, params) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 72, in _execute_on_connection return connection._execute_ddl(self, multiparams, params) File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1073, in _execute_ddl compiled, File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1317, in _execute_context e, statement, parameters, cursor, context File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1511, in _handle_dbapi_exception sqlalchemy_exception, with_traceback=exc_info[2], from_=e File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 182, in raise_ raise exception File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1277, in _execute_context cursor, statement, parameters, context File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 593, in do_execute cursor.execute(statement, parameters) sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) database is locked [SQL: CREATE TABLE layout_info ( root VARCHAR NOT NULL, absolute_paths BOOLEAN, _derivatives VARCHAR, _config VARCHAR, PRIMARY KEY (root), CHECK (absolute_paths IN (0, 1)) ) ] (Background on this error at: http://sqlalche.me/e/13/e3q8) After re-run fmriprep, these subjects have not run fmriprep yet: 'sub-Sub001' 'sub-Sub002' 'sub-Sub003' Error using DPABISurf_run (line 519) Error detected during running fmriprep, please check! Error in DPABISurf_Pipeline>pushbuttonDPABISurfRun_Callback (line 1693) [Error, Cfg]=DPABISurf_run(handles.Cfg); Error in gui_mainfcn (line 95) feval(varargin{:}); Error in DPABISurf_Pipeline (line 42) gui_mainfcn(gui_State, varargin{:}); Error in @(hObject,eventdata)DPABISurf_Pipeline('pushbuttonDPABISurfRun_Callback',hObject,eventdata,guidata(hObject)) Error while evaluating UIControl Callback