FMRIB Software Library (FSL)

Download FSL from the web, run the setup, then use X11 to run it, simply type in fsl

Data needs be to converted to NIfTI format and merged into one 4D file, this can be done using fslchfiletype and fslmerge before beginning analysis and before starting FSL

Data for multiple subjects can be loaded at once and the same job will be applied to all data

Used fMRI Expert Analysis Tool (FEAT)

1.	Click on FEAT fMRI analysis to open the job

2.	Under Data specify the number of datasets under 'Number of inputs' (Each subject should have a single 4D file, data for multiple subjects can be entered and the same job will be applied to them all)

3.	Select the output directory, specify the total volumes, Delete volumes (number of volumes to be ignored to account for T1 effects), the TR (the repetition time for your experiment) and the High pass filter cutoff

4.	Under Pre-stats change the spatial smoothing if required and change any other parameters you may feel necessary (e.g. if you want to run MELODIC ICA) (Leaving as the default setup should be fine)

5.	Under Stats specify whether you want prewhitening, add motion parameters or add any additional confounds

6.	To specify the design of the task either go to Model setup wizard and click on the appropriate design or go to Full model setup and specify conditions, their onsets and durations

7.	Under Post-stats specify any masking you might want, and choose your activation threshold, whether you want uncorrected results, voxel-level correction or cluster-level results and select the p-value you want and how you want your image rendered (displayed on the T1 template) and whether you want time series plots (Leaving all this section as default is probably fine)

8.	Under registration select whether you want to register to standard space using the template or the subject's T1 image (again leaving this as the default is probably fine)

Save this job and run it. FSL will now align and register the data (very similar to what SPM does). A new folder with a .feat appendix will be produced.

Note that if you want to interrogate your data with different thresholds you will need to run the Post-stats again. (Select Post-stats from the top right menu)

Second level analysis

1.	In the FEAT window change First-level analysis to Higher-level analysis

2.	Under Data, select the number of inputs (number of subjects) and select the FEAT directories for all subjects and specify the output directory

3.	Under stats, select the type of model (probably leave as Mixed effects: FLAME 1 is best), go to Model setup wizard to specify whether you have want to do a one-sample t-test, independent samples t-test or paired t-test and then go to Full model setup for any further model setup

4.	Under Post-stats, as before specify the threshold for displaying the activations and options for rendering the images and creating time series. As before if you then want to interrogate the data at a different threshold the Post-stats will need to be run again (select Post-stats from top-right menu)