BIDS convert error for DWI with two reverse coding

suming · August 12, 2022, 3:02pm

dear developers:
Hi!
I met an error when convert dicom image to BIDS file via heudiconv docker. My raw data contain reverse_phase encode DWI image(e.g. LR direction and RL direction). and this is the detail error description.
could anyone give some suggestion for fix the error?
thanks a lot!
suming

File Path: 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 GitHub - bids-standard/bids-validator: Validator for the Brain Imaging Data Structure 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.

Type:		Error
File:		sub-C002_run-001_dir-LR_dwi.bval
Location:		RawData/sub-C002/dwi/sub-C002_run-001_dir-LR_dwi.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/bids-standard/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-C002_run-001_dir-LR_dwi.bval

Type:		Error
File:		sub-C002_run-001_dir-LR_dwi.bvec
Location:		RawData/sub-C002/dwi/sub-C002_run-001_dir-LR_dwi.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/bids-standard/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-C002_run-001_dir-LR_dwi.bvec

Type:		Error
File:		sub-C002_run-001_dir-LR_dwi.json
Location:		RawData/sub-C002/dwi/sub-C002_run-001_dir-LR_dwi.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/bids-standard/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-C002_run-001_dir-LR_dwi.json

Type:		Error
File:		sub-C002_run-001_dir-LR_dwi.nii.gz
Location:		RawData/sub-C002/dwi/sub-C002_run-001_dir-LR_dwi.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/bids-standard/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-C002_run-001_dir-LR_dwi.nii.gz

Type:		Error
File:		sub-C002_run-001_dir-RL_dwi.bval
Location:		RawData/sub-C002/dwi/sub-C002_run-001_dir-RL_dwi.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/bids-standard/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-C002_run-001_dir-RL_dwi.bval

Type:		Error
File:		sub-C002_run-001_dir-RL_dwi.bvec
Location:		RawData/sub-C002/dwi/sub-C002_run-001_dir-RL_dwi.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/bids-standard/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-C002_run-001_dir-RL_dwi.bvec

Type:		Error
File:		sub-C002_run-001_dir-RL_dwi.json
Location:		RawData/sub-C002/dwi/sub-C002_run-001_dir-RL_dwi.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/bids-standard/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-C002_run-001_dir-RL_dwi.json

Type:		Error
File:		sub-C002_run-001_dir-RL_dwi.nii.gz
Location:		RawData/sub-C002/dwi/sub-C002_run-001_dir-RL_dwi.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/bids-standard/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-C002_run-001_dir-RL_dwi.nii.gz

…

======================================================

File Path: The recommended file /README is very small. Please consider expanding it with additional information about the dataset.

Type:		Warning
File:		README
Location:		RawData/README
Reason:		The recommended file /README is very small. Please consider expanding it with additional information about the dataset.

======================================================

Steven · August 12, 2022, 4:18pm

Hi,

Try using run-1 instead of run-001.

Best,
Steven

suming · August 13, 2022, 2:40pm

Hi, Steven
thanks for your suggestion. I followed your advice, however, an error still happend.
which reported Error 1: [Code 1] NOT_INCLUDED
could you please give any additional suggestion?
thanks a lot for your help

suming

File Path: 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 GitHub - bids-standard/bids-validator: Validator for the Brain Imaging Data Structure 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.

Type:		Error
File:		sub-C002_ses-001_run-1_dir-LR_dwi.bval
Location:		RawData/sub-C002/ses-001/dwi/sub-C002_ses-001_run-1_dir-LR_dwi.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/bids-standard/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-C002_ses-001_run-1_dir-LR_dwi.bval

Type:		Error
File:		sub-C002_ses-001_run-1_dir-LR_dwi.bvec
Location:		RawData/sub-C002/ses-001/dwi/sub-C002_ses-001_run-1_dir-LR_dwi.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/bids-standard/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-C002_ses-001_run-1_dir-LR_dwi.bvec

Type:		Error
File:		sub-C002_ses-001_run-1_dir-LR_dwi.json
Location:		RawData/sub-C002/ses-001/dwi/sub-C002_ses-001_run-1_dir-LR_dwi.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/bids-standard/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-C002_ses-001_run-1_dir-LR_dwi.json

Type:		Error
File:		sub-C002_ses-001_run-1_dir-LR_dwi.nii.gz
Location:		RawData/sub-C002/ses-001/dwi/sub-C002_ses-001_run-1_dir-LR_dwi.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/bids-standard/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-C002_ses-001_run-1_dir-LR_dwi.nii.gz

Type:		Error
File:		sub-C002_ses-001_run-1_dir-RL_dwi.bval
Location:		RawData/sub-C002/ses-001/dwi/sub-C002_ses-001_run-1_dir-RL_dwi.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/bids-standard/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-C002_ses-001_run-1_dir-RL_dwi.bval

Type:		Error
File:		sub-C002_ses-001_run-1_dir-RL_dwi.bvec
Location:		RawData/sub-C002/ses-001/dwi/sub-C002_ses-001_run-1_dir-RL_dwi.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/bids-standard/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-C002_ses-001_run-1_dir-RL_dwi.bvec

Type:		Error
File:		sub-C002_ses-001_run-1_dir-RL_dwi.json
Location:		RawData/sub-C002/ses-001/dwi/sub-C002_ses-001_run-1_dir-RL_dwi.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/bids-standard/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-C002_ses-001_run-1_dir-RL_dwi.json

Type:		Error
File:		sub-C002_ses-001_run-1_dir-RL_dwi.nii.gz
Location:		RawData/sub-C002/ses-001/dwi/sub-C002_ses-001_run-1_dir-RL_dwi.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/bids-standard/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-C002_ses-001_run-1_dir-RL_dwi.nii.gz

Steven · August 14, 2022, 4:40pm

Hi,

Try switching the “dir” and “run” order in your file names.

Best,
Steven

suming · September 2, 2022, 10:18am

Hi, Steven
thanks for your advice and it really works

suming