Table 5 Neuroimaging pipelines: frameworks, tools, analysis types, output variables
Processing step | Framework | Tool | Input | Type | Variable/biomarker |
|---|---|---|---|---|---|
Standardization: NII and BIDS conversion | R | BIDSconvertR [15] | dicom | dcm2niix [16] BIDS-conversion | json-metadata, id, birthdate, weight |
Quality control | Docker | MRIQC [8] | T1w, T2w, bold | MRIQC pipeline | See [8] |
Anatomical pipelines | SPM | CAT12 [14] | T1w | VBM | Volume (native/normalized): GM, WM, CSF, WMH + mask |
FSL | fsl_anat | T1w, T2w FLAIR | Anatomical pipeline | Volume (native/normalized): GM, WM, CSF | |
Freesurfer (v6 and v7.1.0) | recon-all (surfer.nmr.mgh.harvard.edu/) | T1w | Cortical thickness | Cortical thickness, ROI-wise | |
Lesion delineation pipelines | SPM | CAT12 [17] | T1w | Lesion segmentation (intensity-based) | Volume (native/normalized): WMH + mask |
FSL | BIANCA [21] | T1w (BET, denoised, FLAIR space) | Lesion segmentation (trained—KNN) | Lesion count + volume (ml) + mask | |
T2w FLAIR (BET, denoised) | |||||
Diffusion-weighted pipelines | FSL | PSMD-Marker [23] | DWI + .bval + .bvec | Diffusion-weighted imaging | PSMD, MSMD, FA/MD (native/normalized and ROI-wise), |
TBSS | |||||
Functional pipelines | Docker | fMRIprep [24] | T1w + bold | Anatomical and functional preprocessing | Structural and functional derivatives; see [24] |
With (disabled Freesurfer processing) |