Repeatability and reproducibility of FreeSurfer, FSL-SIENAX and SPM brain volumetric measurements and the effect of lesion filling in multiple sclerosis.

• The same scanner should be used for brain volumetry. If different scanners are used, the intracranial volume normalisation improves the FreeSurfer and SPM robustness (but not the FSL scaling factor). • FreeSurfer, FSL and SPM all provide robust measures of the whole brain volume on the same MRI scanner. SPM-based methods overall provide the most robust segmentations (except white matter segmentations on different scanners where FreeSurfer is more robust). • MS lesion filling with Lesion Segmentation Toolbox changes the output of FSL-SIENAX and SPM. FreeSurfer output is not affected by MS lesion filling since it already takes white matter hypointensities into account and is therefore particularly suitable for MS brain volumetry.