Bids validator unable to see subject folders

1

Hi,

I’m trying to get my data into bids format to run fmriprep, but I just can’t get past an error where the validator can’t see the subject folders. Can anyone advise what I’m doing wrong?

Output of bids validator:

datapath$ bids-validator .
1: There are no subject folders (labeled “sub-*”) in the root of this dataset. (code: 45 - SUBJECT_FOLDERS)

2: Participant labels found in this dataset did not match the values in participant_id column found in the participants.tsv file. (code: 49 - PARTICIPANT_ID_MISMATCH)
	./participants.tsv
		Evidence: participants.tsv: 10001, 10002, 10003, 10004, 10005, 10006, 10007, 10008, 10009, 10010, 20001, 20002, 20003, 20004, 20005, 20006, 20007, 20009, 20010, 20011, 20012, 20013, 20014, 20015, 20016 folder structure: 

    Summary:                  Available Tasks:        Available Modalities: 
    305 Files, 64.29GB                                                      
    0 - Subjects                                                            
    1 - Session

I’m running it from this directory:

datapath$ ls -l
total 116
-rw-r–r-- 1 tec31 tec31 36 Apr 8 10:59 CHANGES
-rw-r----- 1 tec31 tec31 302 Apr 8 10:54 dataset_description.json
-rw-r–r-- 1 tec31 tec31 165 Apr 8 11:24 participants.tsv
-rw-r–r-- 1 tec31 tec31 15 Apr 5 13:28 README
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-10001
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-10002
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-10003
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-10004
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-10005
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-10006
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-10007
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-10008
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-10009
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-10010
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-20001
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-20002
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-20003
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-20004
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-20005
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-20006
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-20007
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-20009
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-20010
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-20011
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-20012
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-20013
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-20014
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-20015
drwxrwxr-x 3 tec31 tec31 4096 Apr 8 11:02 sub-20016

Bids validator can definitely see inside the folders, as it was giving me errors with my json files and naming conventions, which I have now fixed.

Help gratefully appreciated.

Thomas

2

I fixed the issue, and thought I should say how in case anyone else encounters similar.

Basically, the subject folders only contained datatypes that are not within the bids format (e.g. MP2RAGE structurals), and therefore had to be in .bidsignore . These subject directories were then invisible to the bids validator.

For what it’s worth, I don’t think that this error message is helpful - it would be better to clarify that the directory structure is valid, but there are no visible data. This issue is likely to be encountered more frequently as we move away from simple ‘T1-weighting’ in structural imaging.

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