(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):
...
Later statistics and calculations refer to the cluster index, so this information is typically used repeatedly.
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:
[datauser@localhost temp]$ cluster -i L_Hipp_vertexMNI_rand_tfce_pcorrpp_tstat1.nii.gz -t 0.95-c L_Hipp_vertexMNI_rand_tstat1.nii.gz scalarname="1-p" > cluster_p1.txt
...
{optional: > cluster_corrp.txt}
This produces a similar table to the previous example, but with extra columns showing the cluster values extracted from a second file listed after the "-c" flag. The second input file (t statistic in this example) is referred to as "COPE" (see cluster guide).