# Transforming 5TT image to different space
**URL:** https://community.mrtrix.org/t/transforming-5tt-image-to-different-space/5171
**Category:** Uncategorized
**Created:** [August 31, 2021, 10:07am UTC](https://community.mrtrix.org/t/transforming-5tt-image-to-different-space/5171 "2021-08-31T10:07:41Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@yizhwan](https://community.mrtrix.org/u/yizhwan)
#### Post date: [August 31, 2021, 10:07am UTC](https://community.mrtrix.org/t/transforming-5tt-image-to-different-space/5171/1 "2021-08-31T10:07:41Z")
Hi,
I have a subject scanned twice (time 1 and time 2). Because the time 2 structural scans are poor quality while time 1 structural scans are isotropic voxels I would like to use this subject’s time 1 T1 scan to perform ACT tractography at time 2.
I have already generated a 5TT image from the time 1 T1 scan which works great for ACT tractography at time 1.
Is there a way to register the time 1 5TT image to the time 2 DWI image so I can run tractography?
I have tried to register the time 1 T1 scan to time 2 DWI using ANTS and then running 5ttgen fsl on my transformed image. Although the transformation works very well (first image), the result of 5ttgen fsl is very strange- see attached (bottom image):
Thanks,
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### Author:  [@rsmith](https://community.mrtrix.org/u/rsmith)
#### Post date: [October 24, 2021, 6:05am UTC](https://community.mrtrix.org/t/transforming-5tt-image-to-different-space/5171/2 "2021-10-24T06:05:03Z")
Hi Yizhwan,
> Is there a way to register the time 1 5TT image to the time 2 DWI image so I can run tractography?
You don’t want to _register_ the 5TT image, as the 5TT image is inappropriate to be driving registration. You instead want to register the time 1 T1-weighted image to the time 2 DWI, and then use the computed rigid-body transformation to _transform_ the 5TT image into alignment with the time 2 DWI (or the other way around). See terminology disambiguation [here](https://community.mrtrix.org/t/registration-transformation-regridding-concepts/3684).
> Although the transformation works very well (first image), the result of 5ttgen fsl is very strange- see attached (bottom image):
It’s hard to tell exactly what the complaint is. My first guess is that you’ve provided what looks like a skull-stripped image, but failed to include the `-premasked` option, which means that FSL `bet` will be executed on the data, and probably remove a lot of brain. The tissue decomposition also looks slightly unusual. But I’m not sure how much of this is image quality. Have you perhaps not just applied a rigid-body transformation to the T1-weighted image, but also _resampled_ the T1-weighted image data onto the voxel grid of the DWI? I don’t think it’s of that low a resolution, but the T1-weighted image nevertheless looks somehow … artificial.
Rob