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sotnir / NENAH-BIDS

A collaborate platform for streamlining a BIDS workflow for the NENAH study, on the linux workstation based at University of Southampton.
https://www.southampton.ac.uk/cndng
Creative Commons Zero v1.0 Universal
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MRIQC not working for NENAH-subjects #67

Closed finnlennartsson closed 8 months ago

finnlennartsson commented 3 years ago

$ for file in /local/scratch/disk2/research/NENAH_BIDS/derivatives/preprocessing_logs/NENAH0; do echo -e "\n\n --------------------------------- \n\n basename $file \n"; cat $file/mriqc; done

sub-NENAH002

Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 280, in _index_metadata payload = json.load(handle) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 296, in load parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 348, in loads return _default_decoder.decode(s) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1091 column 3 (char 11880)

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/usr/local/miniconda/bin/mriqc", line 10, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/run.py", line 16, in main parse_args() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/parser.py", line 374, in parse_args config.from_dict(vars(opts)) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 519, in from_dict execution.load(settings) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 185, in load cls.init() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 400, in init re.compile(r"^."), File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 155, in init indexer(self) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 111, in call self._index_metadata() File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 284, in _index_metadata raise IOError(msg) from e OSError: Error occurred while trying to decode JSON from file '/data/rawdata/sub-NENAH017/dwi/sub-NENAH017_dir-PA_run-1_dwi.json'.

sub-NENAH003

Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 280, in _index_metadata payload = json.load(handle) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 296, in load parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 348, in loads return _default_decoder.decode(s) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1091 column 3 (char 11880)

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/usr/local/miniconda/bin/mriqc", line 10, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/run.py", line 16, in main parse_args() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/parser.py", line 374, in parse_args config.from_dict(vars(opts)) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 519, in from_dict execution.load(settings) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 185, in load cls.init() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 400, in init re.compile(r"^."), File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 155, in init indexer(self) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 111, in call self._index_metadata() File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 284, in _index_metadata raise IOError(msg) from e OSError: Error occurred while trying to decode JSON from file '/data/rawdata/sub-NENAH017/dwi/sub-NENAH017_dir-PA_run-1_dwi.json'.

sub-NENAH004

Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 280, in _index_metadata payload = json.load(handle) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 296, in load parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 348, in loads return _default_decoder.decode(s) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1091 column 3 (char 11880)

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/usr/local/miniconda/bin/mriqc", line 10, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/run.py", line 16, in main parse_args() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/parser.py", line 374, in parse_args config.from_dict(vars(opts)) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 519, in from_dict execution.load(settings) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 185, in load cls.init() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 400, in init re.compile(r"^."), File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 155, in init indexer(self) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 111, in call self._index_metadata() File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 284, in _index_metadata raise IOError(msg) from e OSError: Error occurred while trying to decode JSON from file '/data/rawdata/sub-NENAH017/dwi/sub-NENAH017_dir-PA_run-1_dwi.json'.

sub-NENAH005

Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 280, in _index_metadata payload = json.load(handle) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 296, in load parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 348, in loads return _default_decoder.decode(s) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1091 column 3 (char 11880)

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/usr/local/miniconda/bin/mriqc", line 10, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/run.py", line 16, in main parse_args() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/parser.py", line 374, in parse_args config.from_dict(vars(opts)) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 519, in from_dict execution.load(settings) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 185, in load cls.init() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 400, in init re.compile(r"^."), File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 155, in init indexer(self) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 111, in call self._index_metadata() File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 284, in _index_metadata raise IOError(msg) from e OSError: Error occurred while trying to decode JSON from file '/data/rawdata/sub-NENAH017/dwi/sub-NENAH017_dir-PA_run-1_dwi.json'.

sub-NENAH007

Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 280, in _index_metadata payload = json.load(handle) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 296, in load parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 348, in loads return _default_decoder.decode(s) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1091 column 3 (char 11880)

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/usr/local/miniconda/bin/mriqc", line 10, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/run.py", line 16, in main parse_args() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/parser.py", line 374, in parse_args config.from_dict(vars(opts)) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 519, in from_dict execution.load(settings) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 185, in load cls.init() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 400, in init re.compile(r"^."), File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 155, in init indexer(self) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 111, in call self._index_metadata() File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 284, in _index_metadata raise IOError(msg) from e OSError: Error occurred while trying to decode JSON from file '/data/rawdata/sub-NENAH017/dwi/sub-NENAH017_dir-PA_run-1_dwi.json'.

sub-NENAH008

Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 280, in _index_metadata payload = json.load(handle) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 296, in load parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 348, in loads return _default_decoder.decode(s) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1091 column 3 (char 11880)

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/usr/local/miniconda/bin/mriqc", line 10, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/run.py", line 16, in main parse_args() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/parser.py", line 374, in parse_args config.from_dict(vars(opts)) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 519, in from_dict execution.load(settings) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 185, in load cls.init() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 400, in init re.compile(r"^."), File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 155, in init indexer(self) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 111, in call self._index_metadata() File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 284, in _index_metadata raise IOError(msg) from e OSError: Error occurred while trying to decode JSON from file '/data/rawdata/sub-NENAH017/dwi/sub-NENAH017_dir-PA_run-1_dwi.json'.

sub-NENAH010

Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 280, in _index_metadata payload = json.load(handle) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 296, in load parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 348, in loads return _default_decoder.decode(s) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1091 column 3 (char 11880)

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/usr/local/miniconda/bin/mriqc", line 10, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/run.py", line 16, in main parse_args() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/parser.py", line 374, in parse_args config.from_dict(vars(opts)) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 519, in from_dict execution.load(settings) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 185, in load cls.init() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 400, in init re.compile(r"^."), File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 155, in init indexer(self) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 111, in call self._index_metadata() File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 284, in _index_metadata raise IOError(msg) from e OSError: Error occurred while trying to decode JSON from file '/data/rawdata/sub-NENAH017/dwi/sub-NENAH017_dir-PA_run-1_dwi.json'.

sub-NENAH011

Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 280, in _index_metadata payload = json.load(handle) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 296, in load parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 348, in loads return _default_decoder.decode(s) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1091 column 3 (char 11880)

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/usr/local/miniconda/bin/mriqc", line 10, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/run.py", line 16, in main parse_args() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/parser.py", line 374, in parse_args config.from_dict(vars(opts)) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 519, in from_dict execution.load(settings) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 185, in load cls.init() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 400, in init re.compile(r"^."), File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 155, in init indexer(self) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 111, in call self._index_metadata() File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 284, in _index_metadata raise IOError(msg) from e OSError: Error occurred while trying to decode JSON from file '/data/rawdata/sub-NENAH017/dwi/sub-NENAH017_dir-PA_run-1_dwi.json'.

sub-NENAH012

Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 280, in _index_metadata payload = json.load(handle) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 296, in load parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 348, in loads return _default_decoder.decode(s) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1091 column 3 (char 11880)

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/usr/local/miniconda/bin/mriqc", line 10, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/run.py", line 16, in main parse_args() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/parser.py", line 374, in parse_args config.from_dict(vars(opts)) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 519, in from_dict execution.load(settings) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 185, in load cls.init() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 400, in init re.compile(r"^."), File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 155, in init indexer(self) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 111, in call self._index_metadata() File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 284, in _index_metadata raise IOError(msg) from e OSError: Error occurred while trying to decode JSON from file '/data/rawdata/sub-NENAH017/dwi/sub-NENAH017_dir-PA_run-1_dwi.json'.

sub-NENAH014

Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 280, in _index_metadata payload = json.load(handle) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 296, in load parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 348, in loads return _default_decoder.decode(s) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1091 column 3 (char 11880)

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/usr/local/miniconda/bin/mriqc", line 10, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/run.py", line 16, in main parse_args() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/parser.py", line 374, in parse_args config.from_dict(vars(opts)) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 519, in from_dict execution.load(settings) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 185, in load cls.init() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 400, in init re.compile(r"^."), File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 155, in init indexer(self) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 111, in call self._index_metadata() File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 284, in _index_metadata raise IOError(msg) from e OSError: Error occurred while trying to decode JSON from file '/data/rawdata/sub-NENAH017/dwi/sub-NENAH017_dir-PA_run-1_dwi.json'.

sub-NENAH015

Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 280, in _index_metadata payload = json.load(handle) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 296, in load parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 348, in loads return _default_decoder.decode(s) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1091 column 3 (char 11880)

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/usr/local/miniconda/bin/mriqc", line 10, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/run.py", line 16, in main parse_args() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/parser.py", line 374, in parse_args config.from_dict(vars(opts)) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 519, in from_dict execution.load(settings) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 185, in load cls.init() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 400, in init re.compile(r"^."), File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 155, in init indexer(self) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 111, in call self._index_metadata() File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 284, in _index_metadata raise IOError(msg) from e OSError: Error occurred while trying to decode JSON from file '/data/rawdata/sub-NENAH017/dwi/sub-NENAH017_dir-PA_run-1_dwi.json'.

sub-NENAH016

Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 280, in _index_metadata payload = json.load(handle) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 296, in load parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 348, in loads return _default_decoder.decode(s) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1091 column 3 (char 11880)

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/usr/local/miniconda/bin/mriqc", line 10, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/run.py", line 16, in main parse_args() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/parser.py", line 374, in parse_args config.from_dict(vars(opts)) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 519, in from_dict execution.load(settings) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 185, in load cls.init() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 400, in init re.compile(r"^."), File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 155, in init indexer(self) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 111, in call self._index_metadata() File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 284, in _index_metadata raise IOError(msg) from e OSError: Error occurred while trying to decode JSON from file '/data/rawdata/sub-NENAH017/dwi/sub-NENAH017_dir-PA_run-1_dwi.json'.

sub-NENAH017

Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 280, in _index_metadata payload = json.load(handle) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 296, in load parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw) File "/usr/local/miniconda/lib/python3.7/json/init.py", line 348, in loads return _default_decoder.decode(s) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1091 column 3 (char 11880)

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/usr/local/miniconda/bin/mriqc", line 10, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/run.py", line 16, in main parse_args() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/parser.py", line 374, in parse_args config.from_dict(vars(opts)) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 519, in from_dict execution.load(settings) File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 185, in load cls.init() File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/config.py", line 400, in init re.compile(r"^."), File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 155, in init indexer(self) File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 111, in call self._index_metadata() File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 284, in _index_metadata raise IOError(msg) from e OSError: Error occurred while trying to decode JSON from file '/data/rawdata/sub-NENAH017/dwi/sub-NENAH017_dir-PA_run-1_dwi.json'.

finnlennartsson commented 3 years ago

This is because the dwi-PA for subject NENAH017 is faulty! The .JSON file is corrupt

yukaizou2015 commented 3 years ago

This is because the dwi-PA for subject NENAH017 is faulty! The .JSON file is corrupt

2: [ERR] Not a valid JSON file. (code: 27 - JSON_INVALID)
                ./sub-NENAH017/dwi/sub-NENAH017_dir-PA_run-1_dwi.json
                        @ line: 1091 character: 10
                        Evidence:               -nan,
                ./sub-NENAH017/dwi/sub-NENAH017_dir-PA_run-1_dwi.json
                        @ line: 1631 character: 10
                        Evidence:               -nan,
                ./sub-NENAH017/dwi/sub-NENAH017_dir-PA_run-1_dwi.json
                        @ line: 1650 character: 10
                        Evidence:               -nan,
                ./sub-NENAH017/dwi/sub-NENAH017_dir-PA_run-1_dwi.json
                        @ line: 1927 character: 10
                        Evidence:               -nan,
yukaizou2015 commented 3 years ago

(From Syngo) The only two image series of PA are b=1000 (25 and 28 below), no b=2600 series were found. Full output from mrinfo:

   0 -    3 MR images 12:23:47 localizer (*fl2d1) [3] ORIGINAL PRIMARY M ND NORM
   1 -    6 MR images 12:26:08 ep2d_bold_moco_p4_3mm_AP_2170 (*epfid2d1_82) [4] ORIGINAL PRIMARY FMRI NONE ND NORM MOSAIC
   2 -    6 MR images 12:26:08 MoCoSeries (*epfid2d1_82) [5] DERIVED PRIMARY FMRI ND NORM MOCO MOSAIC
   3 -   71 MR images 12:26:59 ep2d_bold_moco_p4_3mm_AP_2170 (*epfid2d1_82) [6] ORIGINAL PRIMARY FMRI NONE ND NORM MOSAIC
   4 -   71 MR images 12:27:00 MoCoSeries (*epfid2d1_82) [7] DERIVED PRIMARY FMRI ND NORM MOCO MOSAIC
   5 -    1 MR images 12:29:15 Design (*epfid2d1_82) [8] DERIVED PRIMARY FMRI DESIGN ND NORM MOCO
   6 -    1 MR images 12:29:15 EvaSeries_GLM (*epfid2d1_82) [9] DERIVED PRIMARY FMRI TTEST ND NORM MOCO MOSAIC GLM
   7 -    3 MR images 12:29:15 Mean_&_t-Maps (*epfid2d1_82) [10] DERIVED PRIMARY FMRI ND NORM MOCO MOSAIC MEAN
   8 -  250 MR images 12:31:33 ep2d_bold_moco_p4_3mm_AP_2170 (*epfid2d1_82) [11] ORIGINAL PRIMARY FMRI NONE ND NORM MOSAIC
   9 -  250 MR images 12:31:33 MoCoSeries (*epfid2d1_82) [12] DERIVED PRIMARY FMRI ND NORM MOCO MOSAIC
  10 -    1 MR images 12:39:45 Design (*epfid2d1_82) [13] DERIVED PRIMARY FMRI DESIGN ND NORM MOCO
  11 -    1 MR images 12:39:45 EvaSeries_GLM (*epfid2d1_82) [14] DERIVED PRIMARY FMRI TTEST ND NORM MOCO MOSAIC GLM
  12 -    3 MR images 12:39:45 Mean_&_t-Maps (*epfid2d1_82) [15] DERIVED PRIMARY FMRI ND NORM MOCO MOSAIC MEAN
  13 -   84 MR images 12:42:46 gre_field_mapping_3mm (*fm2d2r) [16] ORIGINAL PRIMARY M ND
  14 -   84 MR images 12:42:47 gre_field_mapping_3mm (*fm2d2r) [17] ORIGINAL PRIMARY M ND NORM
  15 -   42 MR images 12:42:47 gre_field_mapping_3mm (*fm2d2r) [18] ORIGINAL PRIMARY P ND
  16 -  176 MR images 12:48:56 t1_mprage_sag_p2_iso_1.0 (*tfl3d1_16) [19] ORIGINAL PRIMARY M NORM DIS2D FM3_2 FIL
  17 -   30 MR images 12:49:56 t2_tse_tra_p3_256 (*tse2d1_26) [20] ORIGINAL PRIMARY M ND NORM
  18 -   37 MR images 12:51:50 t2_tse_dark-fluid_FLAIR_cor_p2_4mm (*tir2d1_25) [21] ORIGINAL PRIMARY M ND NORM
  19 -  351 MR images 12:53:39 ep2d_diff_mddw_12_p2_DFC (*ep_b800#10) [22] ORIGINAL PRIMARY DIFFUSION NONE ND NORM DFC
  20 -   27 MR images 12:54:20 ep2d_diff_mddw_12_p2_DFC_ADC (*ep_b0_800) [23] DERIVED PRIMARY DIFFUSION ADC ND NORM DFC
  21 -   27 MR images 12:54:20 ep2d_diff_mddw_12_p2_DFC_TRACEW (*ep_b800t) [24] DERIVED PRIMARY DIFFUSION TRACEW ND NORM DFC
  22 -  160 MR images 12:59:26 t2_spc_da-fl_ax_p2 (*spcir_284ns) [25] ORIGINAL PRIMARY M ND NORM
  23 - 2816 MR images 13:01:46 ep2d_diff_b2600_iso2p3_phase_AP_43dir (*ep_b1000#8) [26] ORIGINAL PRIMARY DIFFUSION NONE ND NORM
  24 -  128 MR images 13:08:16 ep2d_diff_b2600_iso2p3_phase_AP_43dir_TRACEW (*ep_b2600t) [27] DERIVED PRIMARY DIFFUSION TRACEW ND NORM
 ### 25 - 2636 MR images 13:09:00 ep2d_diff_b2600_iso2p3_phase_PA_42dir (*ep_b1000#10) [28] ORIGINAL PRIMARY DIFFUSION NONE ND NORM
  26 - 2816 MR images 13:18:17 ep2d_diff_b2600_iso2p3_phase_AP_43dir (*ep_b1000#42) [29] ORIGINAL PRIMARY DIFFUSION NONE ND NORM
  27 -  128 MR images 13:24:58 ep2d_diff_b2600_iso2p3_phase_AP_43dir_TRACEW (*ep_b1000t) [30] DERIVED PRIMARY DIFFUSION TRACEW ND NORM
 ### 28 - 1762 MR images 13:25:46 ep2d_diff_b2600_iso2p3_phase_PA_42dir (*ep_b1000#3) [31] ORIGINAL PRIMARY DIFFUSION NONE ND NORM

To do: Double check this case on Syngo to see whether b=2600 series exist.

finnlennartsson commented 8 months ago

Not relevant anymore