Source data / raw data

6.0

  • Mismatched data: In the ABCD 6.0 release, there is a mismatch between the tabulated and BIDS (sourcedata and rawdata) in the anonymized MRI scanner serial numbers.

Overview

The sourcedata and rawdata datasets in the data release utilizes the Brain Imaging Data Structure (BIDS) standard for data organization. We provide BIDS formatted anatomical MRI images (T1w and T2w), functional MRI images with spin-echo field maps, and diffusion-weighted images with field maps, organized within the following folder structure. The BIDS directories includes separate folders for each modality:

|__ rawdata/ 
    |__ participants.tsv
    |__ participants.json 
    |__ sessions.json 
    |__ sub-<label>/
        |__ sessions.tsv/
        |__ ses-<label>/
            |__ anat/
            |__ dwi/
            |__ fmap/
            |__ func/

Dataset, Session & Scan-Level Data

Dataset-Level

For rawdata, the participants.tsv file includes all participant IDs and their sex.

Scan-Level

For both sourcedata and rawdata, session-level information is included in the scans.tsv files located within the subject folders and includes filename, acquisition time, type, usable, complete, and QC values like quality (0/1), compliant (0/1) and notes.

Session-Level

For both sourcedata and rawdata, session-level information is included in the sessions.tsv files located within the subject folders and includes session ID and acquisition time.

Source data DICOM file sharing

Unprocessed imaging data are made publicly available in DICOM format in a “source data” BIDS directory structure. DICOM files are packaged in individual archive files (.dicom, .tgz) for each series and arranged in BIDS-compliant directory trees. Metadata are provided in JSON-format text files. For task-fMRI series, also included are the files containing stimulus and behavioral response timing information exported from the stimulus program (E-Prime). Source DICOM data may be shared prior to quality control or curation.

The following DICOM fields are anonymized to de-identify sensitive patient information: SourceApplicationEntityTitle, InstitutionName, OperatorsName, InstitutionAddress, AccessionNumber, ReferringPhysicianName, ReferringPhysicianAddress, ReferringPhysicianTelephoneNumber, ReferringPhysicianIDSequence, ReferencedSOPInstanceUID, StationName, InstitutionalDepartmentName, PhysicianOfRecord, PhysicianOfRecordIDSequence, PerformingPhysiciansName, PerformingPhysiciansIDSequence, NameOfPhysicianReadingStudy, PhysicianReadingStudyIDSequence, ServiceID, MobileLocationNumber, SuiteID, IssuerOfPatientID, PregnancyStatus, PatientBirthDate, OtherPatientIDs, OtherPatientNames, PatientsAge, PatientsSize, PatientsWeight, MedicalRecordLocator, CountryOfResidence, RegionOfResidence, PatientsTelephoneNumbers, EthnicGroup, Occupation, AdditionalPatientsHistory, PatientAddress, PatientsSex, PatientComments, ImageComments, StudyID, PrimaryReceiverSuiteAndHost, RequestingPhysician, CurrentPatientLocation, PatientsInstitutionResidence, SchedulePerformingPhysiciansName}, , PerformedStationAETitle}, , PerformedStationName, PerformedLocation, PerformedProcedureStepStartDate, PerformedProcedureStepStartTime, PerformedProcedureStepID, PerformedProcedureStepDescripton, IssueDateofImagingServiceRequest, DateTime, Date, Time and PersonName.

Siemens normalized sMRI DICOMs

Siemens scanners provide an intensity normalization procedure to correct for bias fields. As a result, Siemens scanners have two sets of DICOMs for each sMRI data series (i.e. T1, T2, T1_NORM, and T2_NORM). The non-normalized images with large intensity ranges (e.g. with a 64 channel head coil) may be clipped at 4095, impairing cortical reconstruction. The ABCD pipeline uses only the normalized sMRI (T1_NORM and T2_NORM), but both versions are included in the source data DICOMs and raw data NIfTI files.

dMRI gradient tables for dMRI DICOMs

Raw diffusion gradient tables (b values and vectors) per scanner manufacturer can be downloaded here:

These gradient tables are provided for convenience and reference. Diffusion directions are also included as bvecs/bvals files in the source and raw data BIDS structures.

Additional notes related to diffusion gradient tables:

  • Prior to software version DV29, GE scanners did not encode the correct multishell gradient table into the DICOM header; a generic single-shell gradient table was encoded instead.
  • These gradient tables are only for use with unprocessed dMRI data. For minimally processed data, new vector tables are generated following motion correction and provided with the minimally processed data.
  • For GE, there are two different versions of the bvecs/bvals files, labeled “DV25” and “DV26”. The “DV25” version is specific to scans acquired with SoftwareVersion DV25. For all other software versions (DV26, DV28, DV29), the “DV26” files will work.
  • For GE, prior to DV29, the diffusion values are not correct in the DICOM header and need to come from an external file (such as a bvec/bval file). As of DV29, the correct diffusion directions can be found in the DICOM header, so no external bvec/bval file is needed if you have the dcm files.
  • For Siemens and Philips, the correct diffusion values can be found in the DICOM header.

Siemens slice timing error

Some Siemens fMRI data have been reported to have negative values for the Siemens CSA slice timing parameter which can prevent the conversion of DICOMs files in some software. This issue has been overcome in some software (e.g. current version of dcm2niix available for download at https://github.com/rordenlab/dcm2niix).

Raw data NIfTI file sharing

Unprocessed imaging data are also made publicly available in NIfTI format in a “raw data” BIDS directory structure. Metadata are included in JSON-format text files. For task-fMRI series, also included are BIDS-compliant events.tsv files containing stimulus and behavioral response timing information extracted from the source data event timing files (i.e., exported from E-prime). For dMRI series, also included are bvecs and bvals files for use in diffusion modeling.

Structural MRI

Anatomical files include T1- and T2-weighted MRI images organized under the anat/ folder of each subject and session. In the event that normalized files were not present, files that had not undergone normalization (e.g. sub-<label>_ses-<label>_T1w.nii.gz) were used instead.

...
|__ anat/
|   |__ sub-<label>_ses-<label>_(rec-norm_)_run-<label>_T1w.nii.gz 
|   |__ sub-<label>_ses-<label>_(rec-norm_)_run-<label>_T1w.json
|   |__ sub-<label>_ses-<label>_(rec-norm_)_run-<label>_T2w.nii.gz
|   |__ sub-<label>_ses-<label>_(rec-norm_)_run-<label>_T2w.json

Functional MRI

Functional files include BOLD functional runs acquired for each task under the func/ folder (including task- MID, nback, SST, and rest, as available) as well as corresponding EPI fieldmaps acquired in AP (dir-AP) and PA (dir-PA) phase encoding directions under fmap/. The functional fieldmaps can be distinguished from DWI fieldmaps via the acq-func tag in the filenames.

...
|__ func/
|   |__ sub-<label>_ses-<label>_task-<mid|nback|sst|rest>_run-<label>_bold.nii.gz
|   |__ sub-<label>_ses-<label>_task-<mid|nback|sst|rest>_run-<label>_bold.json
|
|__ fmap/
|   |__ sub-<label>_ses-<label>_acq-func_dir-<AP/PA>_run-<label>_epi.nii.gz
|   |__ sub-<label>_ses-<label>_acq-func_dir-<AP/PA>_run-<label>_epi.json

For Siemens and GE scan sessions there will be a preference for normalized scans (if present) and non-normalized scans are removed, else non-normalized scans (if present) are preferred. This may cause either normalized or non-normalized scans to be removed from the anat/ folder.

Field Map Selection

Fieldmaps are utilized during image preprocesing to correct for distortions in the phase encoding direction of each fMRI volume using FSL’s topup for details). Fieldmaps are linked to functional (func/ folder) or diffusion (dwi folder) scans based on which one is closer chronologically (i.e., the fieldmap closest in time before a functional or diffusion scan). Only field maps that are marked as usable (i.e., with the “scan_usable” QC flag set to 1) in their related scans.tsv file are used when linking to functional or diffusion scans. Since fieldmaps can be linked to more than one scan, the IntendedFor and B0FieldIdentifier fields are set in their sidecar JSONs.

Diffusion-Weighted Imaging

Diffusion files include DWI (*_dwi.nii.gz) as well as associated bval and bvec files with information about the strength of the diffusion gradient applied during each volume and diffusion gradients directions, respectively. The diffusion acquisitions also have corresponding fieldmaps, located under fmap/, that can be distinguished from the functional fieldmaps by the acq-dwi tag in their filenames.

...
|__ dwi/
|   |__ sub-<label>_ses-<label>_run-<label>_dwi.bval
|   |__ sub-<label>_ses-<label>_run-<label>_dwi.bvec
|   |__ sub-<label>_ses-<label>_run-<label>_dwi.nii.gz
|   |__ sub-<label>_ses-<label>_run-<label>_dwi.json
|
|__ fmap/
|   |__ sub-<label>_ses-<label>_acq-dwi_dir-<AP/PA>_run-<label>_epi.nii.gz
|   |__ sub-<label>_ses-<label>_acq-dwi_dir-<AP/PA>_run-<label>_epi.json

Values for bval/bvec

During BIDS conversion, the bval and bvec file values associated with the DWI data are typically extracted directly from the DICOMs, as was the case for conversion of data from Siemens and Philips scanner vendors. For GE, these values were provided by the DAIRC.

BIDS Conversion & Validation

DICOMs are converted to BIDS NIfTIs using Chris Rorden Lab dcm2niix. BIDS validation is performed using the official BIDS validator.