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

Dear Dr. Yan

I encountered an error when I ran my data (not have DICOM data, start with FunImg and T1Img) by using DpabiSurf. The data have passed the data organization checcking and successfully converted into BIDS. But, the error was reported during the “Preprocessing with fmriprep” stage for every subject. The error log is the following figure. Since this is not DICOM data, I manually entered TR=2 (but I confirm that this is correct). I confirmed that I have correctly installed the DpbaiSurf as I have successfully run the DemoData (start from FunRaw) posted on this website.

The BIDS directory orgaization like:

            Sub-**
                ses-1
                        func
                                    *** rest_bold.nii & ***rest_bold.json
                        anat
                                   ***T1w.nii (NOT have .json file)
               ses-2
                        func
                                    *** rest_bold.nii & ***rest_bold.json
The ***rest_bold.json file are all same such as:
{"RepetitionTime":2,"SliceTiming":[0,1,0.055556,1.0556,0.11111,1.1111,0.16667,1.1667,0.22222,1.2222,0.27778,1.2778,0.33333,1.3333,0.38889,1.3889,0.44444,1.4444,0.5,1.5,0.55556,1.5556,0.61111,1.6111,0.66667,1.6667,0.72222,1.7222,0.77778,1.7778,0.83333,1.8333,0.88889,1.8889,0.94444,1.9444],"TaskName":"REST"}


Also, I tried to use the same setting option to run an open access data (not have DICOM data). Unfountatly, the same error was encountered. However, these two datasets can successfully run in DPARSF without involving fmriprep. The problem seems to be I used the FunImg instead of the FunRaw that can not available for my dataset?

I also tried to debug according to the error information (provided weblinks). However, I can’t find what error derives from since the DPABISurf is a user-friendly toolbox that invokes the code from fmriprep what I am not familiar with.

Have you encountered similar problems or other people have also asked about this problem? Do you have any suggestions on this problem? Thank you in advance for any help.

The text vertion of the error log:

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-n06/ses-1/func/sub-n06_ses-1_task-rest_bold.nii
                                ./sub-n06/ses-2/func/sub-n06_ses-2_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:
        271 Files, 37.23GB        REST                    T1w                  
        54 - Subjects                                     bold                 
        2 - Sessions                                                            


AttachmentSize
Image icon ERROR LOG65.7 KB

The TR info in your NIfTI files (FunImg) were incorrect. You can change the TR info in your NIfTI files.

Or you can try to add one line in DPABISurf_run.m

Line 488:

Command = sprintf('%s --skip_bids_validation', Command);