To call the FEAT GUI, either run Feat, or run fsl and press the FEAT button.
Now set the filename of the 4D input image (e.g. /users/sibelius/origfunc.hdr) by pressing Select 4D data. You can setup FEAT to process many input images, one after another, as long as they all require exactly the same analysis. Each one will generate its own FEAT directory, the name of which is based on the input data's filename (unless you enter an Output directory name).
Note that if you later run Post-stats or Registration, or if you are running Higher-level Analysis, then instead of selecting 4D data as the input, you select FEAT directories. In this case first set the top two drop-down menus in the GUI and then select the FEAT directory or directories; it is important to select the FEAT directories before setting up anything else in FEAT. This is because quite a lot of FEAT settings are loaded from the first selected FEAT directory, possibly over-writing any settings which you wish to change!
If you are running FEAT from within MEDx and the number of File-based first-level analyses is set to 0 then FEAT will use the selected group page inside the current MEDx folder for analysis, instead of a file on disk.
Total volumes (including volumes to be deleted) is automatically set from the input files chosen.
Now set Delete volumes. These should be the volumes that are not wanted because steady-state imaging is not reached for typically two or three volumes. These volumes are deleted as soon as FEAT is started, so any 4D data output by FEAT will not contain the deleted volumes. Note that Delete volumes should not be used to correct for the time lag between stimulation and the measured response - this is corrected for in the design matrix by convolving the input stimulation waveform with a blurring-and-delaying haemodynamic response function. Most importantly, remember when setting up the design matrix that the timings in the design matrix start at t=0 seconds, and this corresponds to the start of the first image taken after the deleted scans. In other words, the design matrix starts after the deleted scans have been deleted.
Set the TR (time from the start of one volume to the start of the next).
Now set the High pass filter cutoff point (seconds), that is, the longest temporal period that you will allow. A sensible setting in the case of an ABAB or ABACABAC type block design is the (A+B) or (A+B+A+C) total cycle time. For event-related designs the rule is not so simple, but in general the cutoff can typically be reduced at least to 50s.
Note that virtually every timing input in FEAT is set in seconds, not volumes. Total volumes and Delete volumes are exceptions.
Now click on the Stats tab and setup the model and required contrasts (for more detail see below).
When FEAT setup is complete and the Go button is pressed, the setup gets saved in a temporary FEAT setup file. Then a script (called feat - note the lower case) is run which uses the setup file and carries out all the FMRI analysis steps asked for, starting by creating a FEAT results directory, and copying the setup file into here, named design.fsf (this setup file can be later loaded back into FEAT using the Load button).
Once the script has started running you can Exit the FEAT GUI (and even log out of your computer). The analysis will continue until completion, by default showing information about its progress in the Featwatcher GUI.