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- "_vertexNative" ==>> "--useReconNative --useRigidAlign" (volume differences)
- "_vertexNativeScale" ==>> "--useReconNative --useRigidAlign --useScale" (shape differences)
- "_vertexMNI" ==>> "--useReconMNI --useRigidAlign" (volume differences accounting for head size)
- "_vertexMNIScale" ==>> "--useReconMNI --useRigidAlign --useScale" (differences after accounting for head size/shape and structure size - hard to interpret but should have the lowest variability)
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 extensions are also created: *.con for t-contrast, *.fts for f-contrast.
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