<> = Initial Processing = Some initial processing of images can help make things work more reliably and accurately in FSL. * All modalities: * Convert from DICOM (using your preferred tool: e.g. `mricron/dicom2nii`, `freesurfer/mri_convert`, etc.) * Check that the conversions are good and that there are no serious artefacts present (open the images in FSLView and spend a couple of minutes looking at them - use the movie loop for functional and diffusion images) * [[Orientation Explained|fslreorient2std]] (assists with future registration steps and makes the views in FSLView more "standard") * Structural images (in addition to the above): * cropping to remove neck and lower head: `robustfov` (automatic) or `fslroi` (manual) * acquisition note: for T1w structurals it is very helpful to have some fat saturation in the T1w sequences to avoid marrow/meninges being mistaken for brain tissue in segmentation and registration