BIDS dataset validator: error in naming files

1

Dear BIDS experts,

Testing online my BIDS folder structure, I got the following error message:

sub-207187M020161011_run-01_corr.bval
0.032 KB |
Location:

Nifti/sub-207187M020161011/dwi/sub-207187M020161011_run-01_corr.bval
Reason:

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/INCF/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.
Evidence:

sub-207187M020161011_run-01_corr.bval
sub-207187M020161011_run-01_corr.bvec
0.113 KB |
Location:

Nifti/sub-207187M020161011/dwi/sub-207187M020161011_run-01_corr.bvec
Reason:

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/INCF/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.
Evidence:

sub-207187M020161011_run-01_corr.bvec
sub-207187M020161011_run-01_corr.json
1.476 KB | application/json
Location:

Nifti/sub-207187M020161011/dwi/sub-207187M020161011_run-01_corr.json
Reason:

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/INCF/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.
Evidence:

sub-207187M020161011_run-01_corr.json
sub-207187M020161011_run-01_corr.nii.gz
3343.26 KB | application/gzip
Location:

Nifti/sub-207187M020161011/dwi/sub-207187M020161011_run-01_corr.nii.gz
Reason:

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/INCF/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.
Evidence:

sub-207187M020161011_run-01_corr.nii.gz
sub-207187M020161011_dir-WIP B0 map CLEAR_run-01_epi.json
13.056 KB | application/json
Location:

Nifti/sub-207187M020161011/fmap/sub-207187M020161011_dir-WIP B0 map CLEAR_run-01_epi.json
Reason:

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/INCF/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.
Evidence:

sub-207187M020161011_dir-WIP B0 map CLEAR_run-01_epi.json
sub-207187M020161011_dir-WIP B0 map CLEAR_run-01_epi.nii.gz
768.856 KB | application/gzip
Location:

Nifti/sub-207187M020161011/fmap/sub-207187M020161011_dir-WIP B0 map CLEAR_run-01_epi.nii.gz
Reason:

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/INCF/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.
Evidence:

sub-207187M020161011_dir-WIP B0 map CLEAR_run-01_epi.nii.gz
sub-207187M020161011_task-rest_run-01_corrap.json
10.843 KB | application/json
Location:

Nifti/sub-207187M020161011/func/sub-207187M020161011_task-rest_run-01_corrap.json
Reason:

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/INCF/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.
Evidence:

sub-207187M020161011_task-rest_run-01_corrap.json
sub-207187M020161011_task-rest_run-01_corrap.nii.gz
185.73 KB | application/gzip
Location:

Nifti/sub-207187M020161011/func/sub-207187M020161011_task-rest_run-01_corrap.nii.gz
Reason:

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/INCF/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.
Evidence:

sub-207187M020161011_task-rest_run-01_corrap.nii.gz
sub-207187M020161011_task-rest_run-01_corrpa.json
10.851 KB | application/json
Location:

Nifti/sub-207187M020161011/func/sub-207187M020161011_task-rest_run-01_corrpa.json
Reason:

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/INCF/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.
Evidence:

sub-207187M020161011_task-rest_run-01_corrpa.json
sub-207187M020161011_task-rest_run-01_corrpa.nii.gz
186.375 KB | application/gzip
Location:

Nifti/sub-207187M020161011/func/sub-207187M020161011_task-rest_run-01_corrpa.nii.gz
Reason:

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/INCF/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.
Evidence:

sub-207187M020161011_task-rest_run-01_corrpa.nii.gz

I have for distortion correction 2 more inverse phase acquisitions corresponding to RS-fMRI run, and 1 more for DTI run. How could I include them “legally” as BIDS dataset ?

Moreover it seems that my B0 map is don’t recognize as fmap ?

Thank you for your help !

Best,
Matthieu

2

Hi @mattvan83,

Those trailing _corr and _corrap, _corrpa are not BIDS valid.

Then, for sub-207187M020161011_dir-WIP B0 map CLEAR_run-01_epi.nii.gz, the general problem is that BIDS label (and particularly the dir-<label>) do not accept spaces, underscores or hyphens. For the acceptable values for the label of the dir- entity, please go to sec 8.3.5.4 of the specification:

dir_label value can be set to arbitrary alphanumeric label ([a-zA-Z0-9]+ for example “LR” or “AP”) that can help users to distinguish between different files, but should not be used to infer any scanning parameters (such as phase encoding directions) of the corresponding sequence. Please rely only on the JSON file to obtain scanning parameters. _epi files can be a 3D or 4D - in the latter case all timepoints share the same scanning parameters. To indicate which run is intended to be used with which functional or diffusion scan the IntendedFor field in the JSON file should be used.

3

Hi @oesteban,

Thank you for your reply.

Concerning dir-label I will look at Bids specifications you mentioned. However, these nifti files are automatically generated by heudiconv, so should I modify systematically nifti names after generation ?

About SDCorrection I have a pair of SE EPI images with reverse phase encoding direction in addition of the RS-fMRI images. How should I set in this case heuristic to be correct regarding BIDS format ?

Same question regarding DTI but I only have one reverse PE direction volume in addition of the 4D dwi files ?

Thanks !

4

I would suggest you to open a new question, where you explicitly mention that it is related to heudiconv.

That way, the responses from @mgxd will be more accessible to other users having the same questions.

In general, if you do not have proper settings in the heuristics file you’ll probably won’t get BIDS compliant results from heudiconv.

5

Thank you I have created a new post:

1 Like
6

Can you link to the new post?

7

Linking to the new post edited above.