Freesurfer mri_convert

Does freesurfer mri_convert takes into consideration the aliasing effect when downsampling images?? Meaning if it blurs the image before downsampling them??

Hi @jagruti8,

I am not sure, but this might be a better question for the FreeSurfer mailing board.


Hi @Steven,

Thanks a lot for the reply.

With best regards,
Jagruti Patel

You need to be careful whenever you downsample an image that you do not have aliasing artifacts. In general, it is better to blur images a little bit rather than allow high frequencies (above the Nyquist) to appear as false lower frequencies.

You can test this yourself by

  1. creating a 512x512x512 voxel zone plate NIfTI
  2. Adjusting the header so that the voxel size is 0.5mm (256mm FOV).
  3. Have FreeSurfer convert it to a 256x256x256 voxel image retaining the 256mm FOV mri_convert -c zoneplate3d_512.nii zoneplate256.nii
  4. Inspect the orginal (left) and conformed (right) image. To me it looks like FreeSurfer has done an admirably job of minimizing the aliasing banding suggesting effective blurring. While one can blur the image before downsampling, a computationally more efficient approach is to simply stretch the interpolation filter with the reduction factor as described by Schumacher. For comparison, you can generate your own unsmoothed donwsampling.