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