Thanks, Mark. I noticed that some subjects did not have the grey matter correctly segmented in SIENAX. I re-ran it using the T1_biascorr.nii.gz from the fsl-anat pipeline as input, and then the segmentation looked much better. Seems like the best approach is to use both commands - fsl-anat to generate the bias-field corrected T1 then run SIENAX on it?
Cheers.
Estephan
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