# Dilating of brain mask and some other general queries

**URL:** <https://community.mrtrix.org/t/dilating-of-brain-mask-and-some-other-general-queries/1304>\
**Category:** Uncategorized\
**Tags:** connectomics, tractography\
**Created:** [November 13, 2017, 6:29am UTC](https://community.mrtrix.org/t/dilating-of-brain-mask-and-some-other-general-queries/1304 "2017-11-13T06:29:07Z")\
**Posts on this page:** 1\
**Showing post:** 9

<div class="post-metadata">

**Author:** ![Michiko](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/m/4bbf92/32.png) [@Michiko](https://community.mrtrix.org/u/Michiko)\
**Post date:** [November 21, 2017, 8:58pm UTC](https://community.mrtrix.org/t/dilating-of-brain-mask-and-some-other-general-queries/1304/9 "2017-11-21T20:58:20Z")

</div>

Dear @Antonin_Skoch,

Thanks for being so detailed in your explanations of how to do this - I managed to map the cortical labels onto the volume-based segmentation file successfully.

Before I rerun parts of my analysis, I’d like to clarify with regard to the T1w\_acpc\_dc\_restore\_brain.nii.gz within the HCP subject 100307’s T1w folder. In the tutorial, it states that we could just run 5ttgen on this file. However, I understand from [other threads](https://community.mrtrix.org/t/beginner-connectome-pipeline-updated/373/4) that we would need the T1 to be transformed to diffusion space before running 5ttgen. However, when I checked, this file’s pixel dimensions are 0.7x0.7x0.7mm whereas the data.nii.gz (diffusion image file) has pixel dimensions of 1.25x1.25x1.25mm. Is this right, or am I using the wrong files to follow the tutorial? The aparc+aseg.nii.gz file also follows 0.7x0.7x0.7mm.

Side note: There is also another T1 file called T1w\_acpc\_dc\_restore\_1.25.nii.gz within the diffusion folder that has not been through skull strip. The pixel dimensions for this file is 1.25x1.25x1.25.

I guess it’s a little confusing both because the HCP data folder contains varying files that are similar, and in the tutorial it states “Note that it is not necessary to use a tissue-segmented image that has the same resolution as the diffusion images”. Thus it’s a little confusing whether registration and transformation to diffusion space is needed?

Thanks, I really appreciate your help! Maybe some others who wrote the tutorial can chime in as well.

Best wishes,  
M.

---

_[View the full topic](https://community.mrtrix.org/t/dilating-of-brain-mask-and-some-other-general-queries/1304)._