The fib file construction from NIFTI files

[Tony Lee]

Hello, dear Frank,

I'm a PhD student from Shanghai Jiao Tong University. I use DSI-Studio as my major DTI processing tool in the related work for its brilliant performance.
Now I have a DTI template that only includes the NIFTI format images (i.e., 4D DTI_tensor.nii.gz,  DTI_V1.nii.gz, 3D DTI_FA.nii.gz, etc.). I want to track fibers from these NIFTI images and construct a fib file to contain the fiber information. I wonder is there any command that I can use for achieving this goal? Or is there any code that I can apply for , to construct a fib file from these NIFTI images?

Thank you so much for your help!

[Frank Yeh]

You may check out the MATLAB section to build a fib file for DSI
Studio: https://dsi-studio.labsolver.org/doc/cli_data.html
Hope this helps,
Frank

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[Tony Lee]

Yes, it is helpful! Very thanks!

I have created a fib format file and visulized in DSI-Studio. 

There is a confused thing for me. According to my limited understanding, I previously thought the fiber direction is consistent with the 1st eigenvector of DTI tensor. So I used the 1st eigenvector (V1.nii.gz) as the input (computed by FSL) for matrix 'dir0' of fib file. While the fiber directions seem incorrect in visualization.

Is there any compoent missed by me? Can I transform the V1.nii.gz or the tensor file to a correct fiber directions file?

Many thanks!

Zhenghao Li

[Frank Yeh]

> I previously thought the fiber direction is consistent with the 1st eigenvector of DTI tensor. So I used the 1st eigenvector (V1.nii.gz) as the input (computed by FSL) for matrix 'dir0' of fib file.

This is correct.

> Is there any compoent missed by me? Can I transform the V1.nii.gz or the tensor file to a correct fiber directions file?

You have to assign FA to FA0.
Best,
Frank

>
> Many thanks!
> Zhenghao Li
> 在2022年3月21日星期一 UTC+8 04:47:53<Frank Yeh> 写道：
>>
>> You may check out the MATLAB section to build a fib file for DSI
>> Studio: https://dsi-studio.labsolver.org/doc/cli_data.html
>> Hope this helps,
>> Frank
>>
>> On Sun, Mar 20, 2022 at 4:58 AM Tony Lee <lee....@gmail.com> wrote:
>> >
>> > Hello, dear Frank,
>> >
>> > I'm a PhD student from Shanghai Jiao Tong University. I use DSI-Studio as my major DTI processing tool in the related work for its brilliant performance.
>> > Now I have a DTI template that only includes the NIFTI format images (i.e., 4D DTI_tensor.nii.gz, DTI_V1.nii.gz, 3D DTI_FA.nii.gz, etc.). I want to track fibers from these NIFTI images and construct a fib file to contain the fiber information. I wonder is there any command that I can use for achieving this goal? Or is there any code that I can apply for , to construct a fib file from these NIFTI images?
>> >
>> > Thank you so much for your help!
>> >
>> > --
>> > You received this message because you are subscribed to the Google Groups "DSI Studio" group.
>> > To unsubscribe from this group and stop receiving emails from it, send an email to dsi-studio+...@googlegroups.com.
>> > To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/273ba1ff-aeff-4634-9ba6-0663cca0c1a9n%40googlegroups.com.
>
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[Tony Lee]

Thanks for your suggestion. I have assigned FA map to FA0 before. 

Today I compared the exported fiber direction file and the first eigenvector file estimated by FSL. I found the second components of them are oppsite, so I inversed it. I think DSI-Studio and FSL may use different coordinate systems.

The fibers directions are reasonable now. It's beautiful in DSI-Studio.

Thanks for your kind help!

Best wishes,

Zhenghao Li