Table 1.
State-of-the-art neuroimaging offers a large catalog of readily available software tools. FMRIPrep integrates best-in-breed tools for each of the preprocessing tasks that its workflow covers, except for steps implemented as part of the development of fMRIPrep (in-house implementations). Tasks listed on the first column are described in detail in Supplementary Note 1.
| Preprocessing task | fMRIPrep includes | Alternatives (not included within fMRIPrep) |
|---|---|---|
| Anatomical T1w brain-extraction | antsBrainExtraction.sh (ANTs) | bet (FSL), 3dSkullstrip (AFNI), MRTOOL (SPM Plug-in) |
| Anatomical surface reconstruction | recon-all (FreeSurfer) | CIVET, BrainSuite, Computational Anatomy (SPM Plug-in) |
| Head-motion estimation (and correction) | mcflirt (FSL) | 3dvolreg (AFNI), spm_realign (SPM), cross_realign_4dfp (4dfp), antsBrainRegistration (ANTs) |
| Susceptibility-derived distortion estimation (and unwarping) | 3dqwarp (AFNI) | fugue and topup (FSL), FieldMap and HySCO (SPM Plug-ins) |
| Slice-timing correction | 3dTshift (AFNI) | slicetimer (FSL), spm_slice_timing (SPM), interp_4dfp (4dfp) |
| Intra-subject registration | bbregister (FreeSurfer), flirt (FSL) | 3dvolreg (AFNI), antsRegistration (ANTs), Coregister (SPM GUI) |
| Spatial normalization (inter-subject co-registration) | antsRegistration (ANTs) | @auto_tlrc (AFNI), fnirt (FSL), Normalize (SPM GUI) |
| Surface sampling | mri_vol2surf (FreeSurfer) | SUMA (AFNI), MNE, Nilearn |
| Subspace projection denoising (ICA, PCA, etc) | melodic (FSL), ICA-AROMA | Nilearn, LMGS (SPM Plug-in) |
| Confounds | in-house implementation | fsl_motion_outliers (FSL), TAPAS PhysIO (SPM Plug-in) |
| Detection of nonsteady-states | in-house implementation | Ad-hoc implementations, manual setting |