BIDS difficulty for a very-newbie... plz help me

Hello, experts on neuroscience!

I am a very newbie, so I have few difficulties on dicom2niix

cd ./sub-CU009CUMR1R1
ls -R

anat  fmap  func

./anat:
sub-CU009CUMR1R1_T1w.json  sub-CU009CUMR1R1_T1w.nii.gz

./fmap:
sub-CU009CUMR1R1_Imaginary_phase1.json    sub-CU009CUMR1R1_Imaginary_phase2.nii.gz  sub-CU009CUMR1R1_phase2.json       sub-CU009CUMR1R1_Real_phase1.nii.gz
sub-CU009CUMR1R1_Imaginary_phase1.nii.gz  sub-CU009CUMR1R1_phase1.json              sub-CU009CUMR1R1_phase2.nii.gz     sub-CU009CUMR1R1_Real_phase2.json
sub-CU009CUMR1R1_Imaginary_phase2.json    sub-CU009CUMR1R1_phase1.nii.gz            sub-CU009CUMR1R1_Real_phase1.json  sub-CU009CUMR1R1_Real_phase2.nii.gz

./func:
sub-CU009CUMR1R1_task-rest_bold1.json  sub-CU009CUMR1R1_task-rest_bold1.nii.gz  sub-CU009CUMR1R1_task-rest_bold2.json  sub-CU009CUMR1R1_task-rest_bold2.nii.gz

I downloaded some data and want to make a pipeline through nipype. Before then, I want to make my raw file into bids.

{
    "descriptions": [
        {
            "dataType": "anat",
            "modalityLabel": "T1w",
            "criteria": {
                "SeriesDescription": "SAG3D FSPGR 11 Flip 1 NEX"
            }   
        },
        {
            "dataType": "func",
            "modalityLabel": "bold1",
            "customLabels": "task-rest",
            "criteria": {
                "SeriesDescription": "RESTING 180 5 DUM 39 sl",
                "ImageType": ["ORIGINAL", "PRIMARY", "EPI", "NONE"],
                "SeriesNumber": 6
            }
        },
        {
            "dataType": "func",
            "modalityLabel": "bold2",
            "customLabels": "task-rest",
            "criteria": {
                "SeriesDescription": "RESTING 180 5 DUM 39 sl",
                "ImageType": ["ORIGINAL", "PRIMARY", "EPI", "NONE"],
                "SeriesNumber": 13
            }
        },
        {
            "dataType": "fmap",
            "modalityLabel": "phase1",
            "customLabels": "Imaginary",
            "criteria": {
                "SeriesDescription": "B0 Map for BOLD 39 sl",
                "ImageType": ["ORIGINAL", "PRIMARY", "OTHER", "IMAGINARY"],
                "EchoNumber": 1
            }
        },
        {
            "dataType": "fmap",
            "modalityLabel": "phase2",
            "customLabels": "Imaginary",
            "criteria": {
                "SeriesDescription": "B0 Map for BOLD 39 sl",
                "ImageType": ["ORIGINAL", "PRIMARY", "OTHER", "IMAGINARY"],
                "EchoNumber": 2
            }
        },
        {
            "dataType": "fmap",
            "modalityLabel": "phase1",
            "customLabels": "Real",
            "criteria": {
                "SeriesDescription": "B0 Map for BOLD 39 sl",
                "ImageType": ["ORIGINAL", "PRIMARY", "OTHER", "REAL"],
                "EchoNumber": 1
            }
        },
        {
            "dataType": "fmap",
            "modalityLabel": "phase2",
            "customLabels": "Real",
            "criteria": {
                "SeriesDescription": "B0 Map for BOLD 39 sl",
                "ImageType": ["ORIGINAL", "PRIMARY", "OTHER", "REAL"],
                "EchoNumber": 2
            }
        },
        {
            "dataType": "fmap",
            "modalityLabel": "phase1",
            "criteria": {
                "SeriesDescription": "B0 Map for BOLD 39 sl",
                "ImageType": ["ORIGINAL", "PRIMARY", "OTHER"],
                "EchoNumber": 1
            }
        },
        {
            "dataType": "fmap",
            "modalityLabel": "phase2",
            "criteria": {
                "SeriesDescription": "B0 Map for BOLD 39 sl",
                "ImageType": ["ORIGINAL", "PRIMARY", "OTHER"],
                "EchoNumber": 2
            }
        }
    ]
}

I built config file along tutorial like above, but it seems have a lot of problems…

I took a bids-validate but it says there are a lot of problems, so I want to ask you for where should I start to change my config.

Thanks a lot for your help.

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 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.

	Type:		Error
	File:		sub-CU009CUMR1R1_Imaginary_phase1.json
	Location:		dataset/sub-CU009CUMR1R1/fmap/sub-CU009CUMR1R1_Imaginary_phase1.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-CU009CUMR1R1_Imaginary_phase1.json

	Type:		Error
	File:		sub-CU009CUMR1R1_Imaginary_phase1.nii.gz
	Location:		dataset/sub-CU009CUMR1R1/fmap/sub-CU009CUMR1R1_Imaginary_phase1.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-CU009CUMR1R1_Imaginary_phase1.nii.gz

	Type:		Error
	File:		sub-CU009CUMR1R1_Imaginary_phase2.json
	Location:		dataset/sub-CU009CUMR1R1/fmap/sub-CU009CUMR1R1_Imaginary_phase2.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-CU009CUMR1R1_Imaginary_phase2.json

	Type:		Error
	File:		sub-CU009CUMR1R1_Imaginary_phase2.nii.gz
	Location:		dataset/sub-CU009CUMR1R1/fmap/sub-CU009CUMR1R1_Imaginary_phase2.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-CU009CUMR1R1_Imaginary_phase2.nii.gz

	Type:		Error
	File:		sub-CU009CUMR1R1_Real_phase1.json
	Location:		dataset/sub-CU009CUMR1R1/fmap/sub-CU009CUMR1R1_Real_phase1.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-CU009CUMR1R1_Real_phase1.json

	Type:		Error
	File:		sub-CU009CUMR1R1_Real_phase1.nii.gz
	Location:		dataset/sub-CU009CUMR1R1/fmap/sub-CU009CUMR1R1_Real_phase1.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-CU009CUMR1R1_Real_phase1.nii.gz

	Type:		Error
	File:		sub-CU009CUMR1R1_Real_phase2.json
	Location:		dataset/sub-CU009CUMR1R1/fmap/sub-CU009CUMR1R1_Real_phase2.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-CU009CUMR1R1_Real_phase2.json

	Type:		Error
	File:		sub-CU009CUMR1R1_Real_phase2.nii.gz
	Location:		dataset/sub-CU009CUMR1R1/fmap/sub-CU009CUMR1R1_Real_phase2.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-CU009CUMR1R1_Real_phase2.nii.gz

	Type:		Error
	File:		sub-CU009CUMR1R1_task-rest_bold1.json
	Location:		dataset/sub-CU009CUMR1R1/func/sub-CU009CUMR1R1_task-rest_bold1.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-CU009CUMR1R1_task-rest_bold1.json

	Type:		Error
	File:		sub-CU009CUMR1R1_task-rest_bold1.nii.gz
	Location:		dataset/sub-CU009CUMR1R1/func/sub-CU009CUMR1R1_task-rest_bold1.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-CU009CUMR1R1_task-rest_bold1.nii.gz

	Type:		Error
	File:		sub-CU009CUMR1R1_task-rest_bold2.json
	Location:		dataset/sub-CU009CUMR1R1/func/sub-CU009CUMR1R1_task-rest_bold2.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-CU009CUMR1R1_task-rest_bold2.json

	Type:		Error
	File:		sub-CU009CUMR1R1_task-rest_bold2.nii.gz
	Location:		dataset/sub-CU009CUMR1R1/func/sub-CU009CUMR1R1_task-rest_bold2.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-CU009CUMR1R1_task-rest_bold2.nii.gz


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


File Path: The compulsory file /dataset_description.json is missing. See Section 03 (Modality agnostic files) of the BIDS specification.

	Type:		Error

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


File Path: Sub label contain an Illegal Character hyphen or underscore. Please edit the filename as per BIDS spec.

	Type:		Error
	File:		sub-CU009CUMR1R1_Imaginary_phase1.json
	Location:		dataset/sub-CU009CUMR1R1/fmap/sub-CU009CUMR1R1_Imaginary_phase1.json
	Reason:		Sub label contain an Illegal Character hyphen or underscore. Please edit the filename as per BIDS spec.
	Evidence:	sub name contains illegal character:/sub-CU009CUMR1R1/fmap/sub-CU009CUMR1R1_Imaginary_phase1.json

	Type:		Error
	File:		sub-CU009CUMR1R1_Imaginary_phase2.json
	Location:		dataset/sub-CU009CUMR1R1/fmap/sub-CU009CUMR1R1_Imaginary_phase2.json
	Reason:		Sub label contain an Illegal Character hyphen or underscore. Please edit the filename as per BIDS spec.
	Evidence:	sub name contains illegal character:/sub-CU009CUMR1R1/fmap/sub-CU009CUMR1R1_Imaginary_phase2.json

	Type:		Error
	File:		sub-CU009CUMR1R1_Real_phase1.json
	Location:		dataset/sub-CU009CUMR1R1/fmap/sub-CU009CUMR1R1_Real_phase1.json
	Reason:		Sub label contain an Illegal Character hyphen or underscore. Please edit the filename as per BIDS spec.
	Evidence:	sub name contains illegal character:/sub-CU009CUMR1R1/fmap/sub-CU009CUMR1R1_Real_phase1.json

	Type:		Error
	File:		sub-CU009CUMR1R1_Real_phase2.json
	Location:		dataset/sub-CU009CUMR1R1/fmap/sub-CU009CUMR1R1_Real_phase2.json
	Reason:		Sub label contain an Illegal Character hyphen or underscore. Please edit the filename as per BIDS spec.
	Evidence:	sub name contains illegal character:/sub-CU009CUMR1R1/fmap/sub-CU009CUMR1R1_Real_phase2.json


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


File Path: The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification.

	Type:		Warning

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



For the phase files I believe the issue comes from the _Imaginary_ part of the file name, that will need to have a proper entity and hyphen to be valid. For field maps acq is the closest appropriate one I can think of, the custom label would be updated to acq-Imaginary
https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#case-2-two-phase-maps-and-two-magnitude-images

For the bold files the issue is coming from the modality label or suffix as its sometimes called. _bold1 and _bold2 are invalid, only _bold. is valid:
https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#task-including-resting-state-imaging-data

To differentiate the files you could move the 1 and 2 into a n entity like run- or acq- There is also a part- entity that may be appropriate:

[_part-<mag|phase|real|imag>]

Complex-valued data MUST be split into one file for each data type. For BOLD data, there are separate suffixes for magnitude (_bold) and phase (_phase) data, but the _phase suffix is deprecated. Newly generated datasets SHOULD NOT use the _phase suffix, and the suffix will be removed from the specification in the next major release. For backwards compatibility, _phase is considered equivalent to _part-phase_bold. When the _phase suffix is not used, each file shares the same name with the exception of the part-<mag|phase> or part-<real|imag> key/value.

1 Like