There are several sources that describe preprocessing in BrainVoyager. First, users can refer to the BrainVoyager User's Guide, which is available both online and offline.
Additionally, users can visit the Brain Innovation helpdesk for detailed information on preprocessing.
The default preprocessing steps for functional data include:
- Slice scan time correction
- 3D motion correction
- Temporal filtering
In addition to these default steps, users can choose to add:
- Mean intensity adjustment
- Spatial smoothing
- EPI distortion correction using specific plugins (either image-registration-based or fieldmap-based)
In the FMR preprocessing dialog, users can review and adjust the specific details of the preprocessing steps.
It is crucial to ensure BrainVoyager correctly interprets the spatial and temporal acquisition parameters extracted from the raw data; only then can accurate preprocessing be performed. If there is an error with any of these data acquisition parameters, users can typically adjust them within the FMR document.
Each preprocessing step not only modifies the data but also updates the name of the newly created FMR/STC document, making it easy to recognize which type of preprocessing has been performed.
In addition to preprocessing at the FMR level, there are options to run certain preprocessing steps on the volume time course (VTC) file. The corresponding dialog can be found in the "Analysis" menu ("VTC Data Preprocessing").
The standard settings for preprocessing generally suit most functional data, but in specific cases, it may be helpful to adjust the settings (e.g., changing the reference volume for motion correction or increasing the number of predictors within the high-pass filtering model).
The order in which preprocessing steps are applied to the data can significantly impact the results. The current order of preprocessing steps is selected to work well for most data.
To change the order of preprocessing steps, users can either manually run the preprocessing steps sequentially by applying each subsequent step to the resulting FMR from the previous step, or they can define the order of preprocessing within a script to automate the process.