- reorient the images to the standard (MNI) orientation [fslreorient2std]
- automatically crop the image [robustfov]
- bias-field correction (RF/B1-inhomogeneity-correction) [FAST]
- registration to standard space (linear and non-linear) [FLIRT and FNIRT]
- brain-extraction [FNIRT-based or BET]
- tissue-type segmentation [FAST]
- subcortical structure segmentation [FIRST]
Hi @Yasmine,
Reorientation like in fslreorient2std
implies the labels (e.g., superior, inferior, etc) are switched to match a convention (e.g., RAS or LPS), but the brain is not warped. It might also imply just a rigid rotation where the brain is not scaled at all.
Registration might mean a more complex operation is happening, in which the brain might be scaled and rotated to match a standard space.
Best,
Steven