BIDS Validator failed: Code 61 Quick validatio failed [and dealing w/ institution_Subjid]

1

Hi community,
I am curious to know what my issue is in the following BIDS format I’ve created:

../datasets$ ls -I *.dcm mydataset/*/*/*/*

mydataset:
dataset_description.json  
rawdata  
sourcedata

mydataset/rawdata/sub-326_500003755/sess-20200930/anat:
sub-326_500003755_sess-20200930_FLAIR.json  
sub-326_500003755_sess-20200930_FLAIR.nii.gz  
sub-326_500003755_sess-20200930_T1w.json  
sub-326_500003755_sess-20200930_T1w.nii.gz

mydataset/sourcedata/sub-326_500003755/sess-20200930/FLAIR:
<...many *dcm files for FLAIR>

mydataset/sourcedata/sub-326_500003755/sess-20200930/T1w:
<...many *dcm files for T1w>

As you can see I have the following notation:
sub-[InstID_SUBJID]_sess-[Date] as my identifiers.

The subject identifier is composed of a 3 num digit specifying the instituion followed by the subject id [9-digit]. Both are connected by _ which may be causing an issue? If this is causing the issues, I am wondering what suggestions you have to replace the _ w/ another character?

2

Hi, a few things:

  1. In typical BIDS format datasets, all of the individual subject folders (what you have in rawdata) would be on the same level as sourcedata and dataset_description.json
  2. There are some other BIDS files, such as README. participants.tsv, that are either recommended or required that I do not see in your folder.
  3. Should be ses, not sess
  4. Your subject labels (what goes after sub-) should not have an underscore in it, as you suggested. I have seen some studies use the session label as the institute (sub-123_ses-institute_....), or you could do a letter/number combo for subject label and institute (like sub-ABC12345) where ABC is a string of letters relating to the institute, and 12345 is the subject number. Alternatively, if it’s always 3 characters for institute and 9 for subject number, then you can even just remove the underscore and use the consistency in naming convention to parse labels in to their institute and subject part when you go to analyze them.
  5. It’s not conventional to put dates of scans in file names, as that can be identifying information.

Hope this helps,
Steven

3

Thank you Steven for your rapid response.

I have incorporated your changes but am still getting the same error. Is there any other insights I am missing?
The folder level I tried to upload is mydataset/ and I also tried mydataset/rawadata/:

mydataset:
    dataset_description.json 
    rawdata/
    README 
    sourcedata/

mydataset/sourcedata:
    sourcedata/sub-326500003755_ses-20200930_FLAIR:
    <...many *.dcm>
    sourcedata/sub-326500003755_ses-20200930_T1w:
    <...many *.dcm>

mydataset/rawdata:
    sub-326500003755_ses-20200930_FLAIR.json 
    sub-326500003755_ses-20200930_FLAIR.nii.gz 
    sub-326500003755_ses-20200930_T1w.json
    sub-326500003755_ses-20200930_T1w.nii.gz

**Also, the date that I use to separate sessions has already been manipulated to avoid identifying information (thanks for pointing this out)

5

Each subjects data should be in a subject specific folder, and within those certain data go in their own folders (eg anat func dwi fmap etc). These folders are on the main level of the directory (that is, not in rawdata). If you still have the Dicoms I suggest using dcm2bids to automate the data organization from raw data to full compliant bids dataset, leave the guesswork out of it!

Best,
Steven

6

https://bids.neuroimaging.io/ Looking through this might be helpful.

7

Thank you Steven. A

fter looking at it, I decided to use dcm2bids to convert my DICOMDIR into the BIDS format.
I have now successfully validated it.

Just to close this question, my data looks like this now:

mydataset:
dataset_description.json
participants.tsv
README
sub-326500003755
tmp_dcm2bids

mspaths005/sub-326MPI500003755/ses-20200930/anat:
sub-326MPI500003755_ses-20200930_FLAIR.json
sub-326MPI500003755_ses-20200930_FLAIR.nii.gz
sub-326MPI500003755_ses-20200930_T1w.json
sub-326MPI500003755_ses-20200930_T1w.nii.gz