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The output of randomise are statistic, p , value, and corrected p values value files, for each contrast. The contrasts to which statistics files correspond are indicated by numbers, e.g., *_tstat1, *_tstat2_tstat1 (or _fstat1), *_tstat2, *_tstat3tstat3, 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". 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 (sometimes 0 causes an error), so it may look like this:
- Under Tools menu, select 3D Viewer
- If you get a message ...vtkDecimatePro.cxx .... "No data to decimate!", this most likely means the thresholds are messed up. Chnage
- Turn Clipping on (check the box on the top-right); this will "cut out" a chunk of the brain. From ehre, you want to adjust this cutout so you see the structure of interest, and enough of the brain to orient you.
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