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The output of this step is a 4D nifti file (*.nii.gz) with the name as indicated in the -o option, and a _mask file with a similar name. Additional files with the same name as the design matrix but with different extenstions are also created: *.con for t-contrast, *.fts for f-contrast, .
Analysis options (from UserGuide)
The --useReconNative option carries out vertex analysis in native space, along with the --useRigidAlign option. The --useReconMNI option may also be used to carry out vertex analysis, it will do it in the MNI standard space instead, which normalises for brain size. It is difficult to say which will be more sensitive to changes in shape, and so it may be interesting to try both the --useReconNative and the --useReconMNI options. Also note that the --useScale option will not be used. Without the --useScale option, changes in both local shape and size can be found in shape analysis. This type of finding can be interpreted, for example, as local atrophy. With the--useScale option, overall changes in size are lost.
Running Analysis
Randomize is like "Results" in SPM in that it does a statistical test on a contrast. The inputs are the outputs from the previous step.
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