(Not updated in 2015) How to quantify results for FSL FIRST, after stats have been generated.
Clusters
For a stats file "L_Hipp_vertexMNI_rand_tfce_p_tstat1.nii.gz" for example, you can get information based on standard FSL reporting (this page has several examples).
The following two commands will get you started:
Defining clusters (see FSL guide)
Example command for corrected p value < 0.05 (which requires a threshold of 0.95 since p values are stored in nifti files as 1-p):
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Tip: if you copy the table and paste into Excel, either from the Linux terminal or from the text file, it will sort into columns properly:
P values and t statistics
Example command to extract t values at significant clusters:
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