Hi Romain, did you also need to generate masks for upsampled/scaled images (e.g. for the fixel based analysis pipeline)? The instructions here say to compute a mask on the upsampled normalised dwi images (scaled to 2.0). Although these images have been bias corrected and normalised, I’m still getting holes when I run:
dwi2mask input_upsampled_dwi output_upsampled_mask
Do you (or anyone else) know if it would be appropriate to do the following instead?
mrresize input_dwi_original_sized_mask -scale 2.0 output_upsampled_dwi_mask