Page Comparison

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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.

More notes from a practical:

• To run vertex analysis, you will need the .bvars files output by FIRST and a design matrix. These contain all the information required by first_utils.
• It sometimes may be desirable to reconstruct the surfaces in native space (i.e. without the affine normalization to MNI152 space). To do this, instead of --useReconMNI, use the --useReconNative and --useRigidAlign options.
• When using the --useRigidAlign flag, first_utils will align each surface to the mean shape (from the model used by FIRST) with 6 degrees of freedom (translation and rotation). The transformation is calculated such that the sum-of-squared distances between the corresponding vertices is minimized. This command is needed when using --useReconNative, however, can be used with --useReconMNI to remove local rigid body differences.
• The --useScale flag can be used in combination with --useRigidAlign to align the surfaces using 7 dof. --useScale will indicate to first_utils to remove global scaling.

Running Analysis

Randomize is like "Results" in SPM in that it does a statistical test on a contrast. The inputs (analysis and mask) are the outputs from the previous step.

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