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The output of randomise are statistic, p value, and corrected p value files, for each contrast. The contrasts to which statistics files correspond are indicated by numbers, e.g., *_tstat1 (or _fstat1), *_tstat2, *_tstat3, and so on. For a two-group design matrix, you will typically have four contrasts; these are listed in the *.con text file created when you create the design matrix with the Glm GUI. Below is an example:
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[user@localhost temp]$ /usr/local/fsl/bin/first3Dview L_Hipp_vertexMNI_2sample_mask.nii.gz L_Hipp_vertexMNI_2sample_rand_tfceclustere_pcorrp_tstat1fstat1.nii.gz
Note: FSLView uses radiological convention, so left on right as in the above example.
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- The p or corrp overlay image (above basestruct) should already be set to Image type "Statistic" but you can check by selecting the image and clicking "i". Change these (e.g., This image is in a "1-p" numerical value (to avoidn technical problems with very small numbers). Thus, a range of 0.95 to 1 corresponds to p = 0.05 to p = 0. To see everything with the slightest A.B (or B>A) difference, change the minimum to 0.0001 for the Min; (sometimes 0 causes this an error), so it may look like this:
- Under Tools menu, select 3D Viewer
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