# Dwi2mask: holes in mask images

**URL:** <https://community.mrtrix.org/t/dwi2mask-holes-in-mask-images/484>\
**Category:** Uncategorized\
**Created:** [October 3, 2016, 5:05pm UTC](https://community.mrtrix.org/t/dwi2mask-holes-in-mask-images/484 "2016-10-03T17:05:56Z")\
**Posts on this page:** 1\
**Showing post:** 9

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**Author:** ![rgrazioplene](https://community.mrtrix.org/user_avatar/community.mrtrix.org/rgrazioplene/32/284_2.png) [@rgrazioplene](https://community.mrtrix.org/u/rgrazioplene)\
**Post date:** [October 4, 2016, 6:31pm UTC](https://community.mrtrix.org/t/dwi2mask-holes-in-mask-images/484/9 "2016-10-04T18:31:57Z")

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Hi Romain, did you also need to generate masks for upsampled/scaled images (e.g. for the fixel based analysis pipeline)? The instructions [here](http://mrtrix.readthedocs.io/en/latest/workflows/fixel_based_analysis.html) 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

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