FSL

## FEAT Programs

- Feat - the FEAT GUI, as described above.
- feat - the FEAT script which the GUI calls when the setup has been completed and GO is pressed. If you have saved a FEAT setup file (eg design.fsf) to file, then you can run FEAT without the GUI by typing feat <featsetupfile.fsf>.
- Glm - a GUI for setting up just the design matrix and contrasts, in the same way as in FEAT, for use with other modelling/inference programs such as randomise.
- easythresh - a simple script for carrying out cluster-based thresholding and colour activation overlaying.
- featregapply - a program which applies the lowres to standard-space registration transforms to the lowres stats images in a FEAT directory to generate standard-space versions, for inputting to higher-level analysis.
- Featquery (GUI) and featquery (command-line script) - a program which allows you to interrogate FEAT results by defining a mask or set of co-ordinates (in standard-space, highres-space or loweres-space) and get mean stats values and time-series.
- feat_model - a program which uses the FEAT setup file to create the required design matrix as a text file, as well as the related design matrix pictures.
- mccutup - convert the estimates of motion saved in a FEAT directory to separate files which can then be fed into FEAT as Custom (1 entry per volume) EVs.
- Renderhighres (GUI) and renderhighres (command-line script) - transforms all thresholded stats images in a FEAT directory into high resolution or standard space and overlays these onto the high resolution or standard space images. This then produces PNG format pictures of the overlays and, by default, deletes the 3D AVW colour overlay images.
- tsplot - create time series plots for a FEAT directory.