ERROR IN DPABISurf: Repetition time did not match between the scan's header and the associated JSON metadata file.

Dear Prof. Yan, 

I comfirm my TR=2 is correct, since this TR setting have successfully been applied in DPARSF. 

I also tried add a command  one line in DPABISurf_run.m Line 488:

But, Similiar error occurred, the log is as following:

Preprocessing with fmriprep, this process is very time consuming, please be patient...

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-n02/func/sub-n02_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: 

        163 Files, 19.21GB        REST                    T1w                   

        54 - 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 "

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/tmp3oezcfe_']' returned non-zero exit status 1.

/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/tmplty1pjyh']' returned non-zero exit status 1.

Can your recommed other possible solutions for this error? Thank you and best wishes!

Zeqiang

Dear Dr. Yan, Thanks for your solution!  

Although the  developing version of DPARSFSurf cannot seem to  solve this error, the problem was resolved by changing the TR info in NIfTI header for every subject in BIDS directory, which is inspired by the code you gave above. Luckly, the DPARSFSurf can successfully run after changing the TR info. The code I used is as following, which maybe helpful for other people who encounter the same error: 

cd '$analysispath\BIDS' 

dir1 = dir('sub*')
parfor i = 1:length(dir1)
    dir2 = dir([dir1(i).name,'\func\sub*.nii'])
    [Data Header] = y_Read([dir1(i).name,'\func\',dir2.name]);
    Header.private.timing.tspace = 2;   %2 is my TR info
    y_Write(Data,Header,[dir1(i).name,'\func\',dir2.name]);
end

Again, thank you for your expensive time on this problem!

Zeqiang