Visualize the fiber tracts generated from MRtrix

[Z S]

Hi Frank,

Recently, I generated fiber tracts from MRtrix and I wanted to show them in DSI Studio (like this).

I tried to learn this visualization from your video. https://www.youtube.com/watch?v=PdjfjRW7bLw  

Step1, I converted the tck file to trk file.

Step2, I loaded the FA map and T1W map into DSI Studio, ran registration.

Step3, I loaded the trk map into DSI Studio. But, I got the following map. So, we can see the brain and fiber tracts are separated.

Do you have any thoughts about this issue?

Thanks,

Zhiqiang

[Fang-Cheng Yeh]

How did you convert from tck to trk?

You may need to shift the coordinates to align the image space.

Frank

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[Z S]

Hi Frank,

Thanks for your suggestions. Get it. I need to use FA.nii.gz as a reference map, rather than T1.nii.gz. Now all is well.

Best,

Zhiqiang

[Katja Heuer]

Hi Frank and Zhiqiang,

I have a similar issue (conversion failed, and loading the tck directly shows them in a different space). Please, could you let me know how you converted from tck to trk? Would you be happy to share the code / command line with me? 

Thank you so much in advance.

Have a lovely Sunday!

Best,

Katja

[Frank Yeh]

Hi Katja,

    The solution depends on the space the tck was created in.

    Is it possible to upload a sample data (tck and fib.gz) so that I can look into the issue?

Best,

Frank

On Sun, Oct 1, 2023 at 5:15 AM Katja Heuer <katja...@gmail.com> wrote:

Hi Frank and Zhiqiang,

I have a similar issue (conversion failed, and loading the tck directly shows them in a different space). Please, could you let me know how you converted from tck to trk? Would you be happy to share the code / command line with me? 

Thank you so much in advance.

Have a lovely Sunday!

Best,

Katja

On Sunday, 18 September 2022 at 11:45:00 UTC+2 Z S wrote:

Hi Frank,

Thanks for your suggestions. Get it. I need to use FA.nii.gz as a reference map, rather than T1.nii.gz. Now all is well.

Best,

Zhiqiang

在2022年9月17日星期六 UTC+2 20:56:21<Frank Yeh> 写道：

How did you convert from tck to trk?

You may need to shift the coordinates to align the image space.

Frank

On Sat, Sep 17, 2022 at 2:17 PM Z S <zhiq...@gmail.com> wrote:

Hi Frank,

Recently, I generated fiber tracts from MRtrix and I wanted to show them in DSI Studio (like this).

I tried to learn this visualization from your video. https://www.youtube.com/watch?v=PdjfjRW7bLw  

Step1, I converted the tck file to trk file.

Step2, I loaded the FA map and T1W map into DSI Studio, ran registration.

Step3, I loaded the trk map into DSI Studio. But, I got the following map. So, we can see the brain and fiber tracts are separated.

Do you have any thoughts about this issue?

Thanks,

Zhiqiang

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