Hi,
I run 'bet' command. Most worked well with few exceptions which all gave the same problem: the 'nodif_brain.nii' and the 'nodif_brain_mask.nii' files created have a big black hole in the frontal part of the interhemispheric fissure (I used f 0.2 to bet).
To solve that I tried:
- reducing the f to 0.1, but it made worse
- increasing the f: it reduced the hole, but has eaten quite a lot of the edges of the brain
- manually created a mask filling this hole, added the new mask to the old mask to use in Eddy (it worked in Eddy). However, it did not help for 'dftfit' as it needs the file 'nodif_brain.nii' to work rather than the mask
What is the way around it?
- Can I 'bet' using the mask that I created somehow?
Regards,
Thais Minett
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