Table 1.
Overview of neuroimaging sequences and parameters.
Fig 1.
Methodological steps applied to each imaging modality in ABRIM.
Schematic illustration of the methodological steps that were applied for each imaging modality, and its corresponding Brain Imaging Data Structure (BIDS) folders of the ABRIM MRI collection. Each column in the figure represents a different imaging modality, and is distinguished by a unique colour (e.g., T1 images in blue). Each row represents a specific methodological step (e.g., fMRIprep [74]) with its corresponding sub-steps (e.g., brain extraction). BIDS folders are denoted with black frames. The process starts with the source data (e.g., bids/subj/anat/ folder) and progresses to the derivatives (e.g., bids/derivatives/fmriprep/ folder). For each imaging modality, an example output image is displayed at the bottom. All code utilized can be found in the bids/code folder. Note that a certain imaging modality may be processed by multiple methods (e.g., T1 images with both fMRIprep and QSIprep [74, 75]). *fmap is available under bids/subj/derivatives/SIEMENS/.
Fig 2.
Example of slicereport output for ABRIM.
An example of the slicereport-tool to create visual quality control reports for Quantitative Susceptibility Mapping (QSM) output in ABRIM. The top left image displays the generated web page, featuring rows of image slices per subject. In this case, the researchers opted for several sagittal, coronal, and axial slices to enable visual inspection of physiological noise (e.g., motion, ringing) and streaking artifacts. Upon clicking on the image slices of a specific subject, it leads to a sub-page (right bottom image). In this case, the sub-page displays a more detailed representation of the various slice orientations to further facilitate visual inspection. To facilitate the delineation of motion artifact, the sub-page additionally contains a weblink that enables the user to view the corresponding R2* maps (“report_R2Starmap/sub-001/sub-001_run-1_desc-subreport_MEGRE_R2starmap.html”).
Fig 3.
Demographics of the ABRIM study by age decade.
The upper section displays the distribution of male and female participants for each age decade. The lower section consists of several pie charts, displaying the relative distribution of participants with low, medium, and high educational attainment within each age decade. Levels of education were classified using the International Classification of Education (ISCED-11): low education (ISCED 0–2), medium education (ISCED 3–4), and high education (ISCED 5–8). Data on educational attainment were not available for n = 18 participants.
Fig 4.
Overview of ABRIM BIDS folder structure.
Hierarchical overview of ABRIM MRI data collection folder structure following the Brain Imaging Data Structure (BIDS) standard. The “code” folder contains all scripts that have been applied for data processing. The “derivatives” folder contains all processed and derived data that has been generated from the raw MRI data (e.g., “NORDIC”, “SEPIA”, etc.). Individual subject-specific folders (e.g., “sub-001”, “sub-002”, etc.) contain modality-specific sub-folders with different types of MRI data (e.g., “anat” contains structural MRI data, whereas “dwi” contains diffusion-weighted imaging data).
Fig 5.
Group report of T1 images from the MRI Quality Control tool.
Group anatomical report of T1 scans in ABRIM as generated by the MRI Quality control tool (MRIQC). Contains separate strip-plots for different image quality metrics (IQMs). CJV, coefficient of joint variation; CNR, contrast-to-noise-ratio; EFC, entropy focus criterion; FBER, foreground-to-background energy ratio; WM2MAX white-matter to maximum intensity ratio; SNR, signal-to-noise-ratio; SNRD, Dietrich’s signal-to-noise-ratio; FWHM (vox), full width half maximum in units of voxels; QI, quality index; INU, intensity non-uniformity; ICVS, intracranial volume fraction; RPVE, residual partial volume effect; TPM_OVERLAP, overlap of issue probability maps of the images and maps from the ICBM nonlinear-asymmetric 2009a template.