Table 7.
Comparing between various vertex-based analysis toolboxes/software.
| VertexWiseR | QDECR ( Lamballais & Muetzel, 2021 ) | BrainStat ( Larivière et al., 2023 ) | FreeSurfer ( Fischl, 2012 ) | CAT12 ( Gaser et al., 2024 ) | TFCE_mediation ( Lett et al., 2017 ) | |
|---|---|---|---|---|---|---|
| Operating systems (outside of dockers/virtual machines) | Windows, Linux, MacOS | Linux, MacOS | Windows, Linux, MacOS | Linux, MacOS | Windows, Linux, MacOS | Linux, MacOS |
| Environment | R | R | Python/MATLAB | CLE | MATLAB GUI | CLE |
| Preprocess raw data | No | No | No | Yes | Yes | No |
| Reads surface data from preprocessed output directories |
Yes
(FreeSurfer, HCP pipeline, HippUnfold, fMRIprep) |
Yes
(FreeSurfer) |
No |
Yes
(FreeSurfer) |
Yes
(CAT12) |
Yes
(FreeSurfer, CIVET) |
| Concatenates all subjects’ data into a single portable file |
Yes
(.rds format) |
No | No |
Yes
(.mgh format) |
No |
Yes
(.mgh format) |
| Surface supported | fsaverage5, fsaverage6,fsLR32k, CIT168 | All fsaverage |
All fsaverage,
fsLR32k, CIVET |
All fsaverage | fsLR32k |
All fsaverage,
CIVET |
| Cluster thresholding procedure | RFT, TFCE | MCS | RFT | MCS | TFCE, FWE, FDR | TFCE |
| Supported statistical models |
Linear,
Mixed-effects |
Linear |
Linear,
Mixed-effects |
Linear,
Mixed-effects |
Linear,
Flexible factorial |
Linear,
Mediation |
| Extract atlas-based ROIs | Yes | No | No | Yes | Yes | No |
| Meta-analytic decoding | Yes | No | Yes | No | No | No |
Note. CLE = command line environment; GUI = graphical user interface; RFT = random field theory; FDR = false discovery rate; TFCE = threshold-free cluster enhancement; MCS = Monte Carlo simulation; FWE = family wise error.