How to solve the error while running for fmriprep?

 

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                             February 23, 2018

 

 

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These subjects have not run fmriprep yet:

    'sub-002S5256'

    'sub-012S5213'

 

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'.

 

bids-validator@1.4.0

 

1: [ERR] Repetition time did not match between the scan's header and the associated JSON metadata file. (code: 12 - REPETITION_TIME_MISMATCH)

./sub-012S5213/func/sub-012S5213_task-rest_bold.nii

 

 Please visit https://neurostars.org/search?q=REPETITION_TIME_MISMATCH for existing conversations about this issue.

 

1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)

 

 Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.

 

2: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered because there are no authors, which will make DOI registration from dataset metadata impossible. (code: 113 - NO_AUTHORS)

 

 Please visit https://neurostars.org/search?q=NO_AUTHORS for existing conversations about this issue.

 

 

        Summary:                 Available Tasks:        Available Modalities: 

        130 Files, 3.75GB        REST                    T1w                   

        43 - Subjects                                    bold                  

        1 - Session                                                            

 

 

 If you have any questions, please post on https://neurostars.org/tags/bids.

 

/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 "

You are using fMRIPrep-20.2.1, and a newer version of fMRIPrep is available: 20.2.3.

Please check out our documentation about how and when to upgrade:

https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading

WARNING: Version 20.2.1 of fMRIPrep (current) has been FLAGGED

(reason: Functional outputs in standard space can be wrong depending on the original data's orientation headers - see https://github.com/nipreps/fmriprep/issues/2307).

That means some severe flaw was found in it and we strongly

discourage its usage.

Traceback (most recent call last):

  File "/usr/local/miniconda/bin/fmriprep", line 10, in <module>

    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 703, in parse_args

    config.environment.exec_env, opts.bids_dir, opts.participant_label

  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/utils/bids.py", line 155, in validate_input_dir

    subprocess.check_call(['bids-validator', bids_dir, '-c', temp.name])

  File "/usr/local/miniconda/lib/python3.7/subprocess.py", line 341, in check_call

    raise CalledProcessError(retcode, cmd)

subprocess.CalledProcessError: Command '['bids-validator', PosixPath('/data/BIDS'), '-c', '/tmp/tmplcjxh8m6']' returned non-zero exit status 1.

bids-validator@1.4.0

 

1: [ERR] Repetition time did not match between the scan's header and the associated JSON metadata file. (code: 12 - REPETITION_TIME_MISMATCH)

./sub-002S5256/func/sub-002S5256_task-rest_bold.nii

 

 Please visit https://neurostars.org/search?q=REPETITION_TIME_MISMATCH for existing conversations about this issue.

 

1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)

 

 Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.

 

2: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered because there are no authors, which will make DOI registration from dataset metadata impossible. (code: 113 - NO_AUTHORS)

 

 Please visit https://neurostars.org/search?q=NO_AUTHORS for existing conversations about this issue.

 

 

        Summary:                 Available Tasks:        Available Modalities: 

        130 Files, 3.75GB        REST                    T1w                   

        43 - Subjects                                    bold                  

        1 - Session                                                            

 

 

 If you have any questions, please post on https://neurostars.org/tags/bids.

 

/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 "

You are using fMRIPrep-20.2.1, and a newer version of fMRIPrep is available: 20.2.3.

Please check out our documentation about how and when to upgrade:

https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading

WARNING: Version 20.2.1 of fMRIPrep (current) has been FLAGGED

(reason: Functional outputs in standard space can be wrong depending on the original data's orientation headers - see https://github.com/nipreps/fmriprep/issues/2307).

That means some severe flaw was found in it and we strongly

discourage its usage.

Traceback (most recent call last):

  File "/usr/local/miniconda/bin/fmriprep", line 10, in <module>

    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 703, in parse_args

    config.environment.exec_env, opts.bids_dir, opts.participant_label

  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/utils/bids.py", line 155, in validate_input_dir

    subprocess.check_call(['bids-validator', bids_dir, '-c', temp.name])

  File "/usr/local/miniconda/lib/python3.7/subprocess.py", line 341, in check_call

    raise CalledProcessError(retcode, cmd)

subprocess.CalledProcessError: Command '['bids-validator', PosixPath('/data/BIDS'), '-c', '/tmp/tmplocsaebv']' returned non-zero exit status 1.

 

After re-run fmriprep, these subjects have not run fmriprep yet:

    'sub-002S5256'

    'sub-012S5213'

 

 

FailedID =

 

     []

 

 

WaitingID =

 

  2x1 cell array

 

    {'sub-002S5256'}

    {'sub-012S5213'}

 

 

SuccessID =

 

     []

 

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