Fiber tract visualised on a glass brain

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You can follow the steps described by Matteo Mancini in Making a glass brain // NeuroSnippets :

  1. upsample the mask
  2. use a Gaussian filter to smooth the upsampled mask
  3. use a threshold to obtain a neat black-and-white result
  4. dilate the previous volume
  5. subtract the volume obtained in point 4 from the dilated volume
mrresize mask.mif -scale 5 mask_up.mif
mrfilter mask_up.mif smooth -stdev 2 mask_smooth.mif
mrthreshold mask_smooth.mif -abs 0.5 mask_thres.mif
maskfilter mask_thres.mif dilate -npass 2 mask_dilated.mif
mrcalc mask_dilated.mif mask_thres.mif -subtract glass_brain.mif

Then open glass_brain.mif with mrview and switch to volume renderer view and play with the alpha settings untill you get the desired effect.

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