automatic fiber tracking for macaque template

[yasaman bagherzadeh]

Hi Frank,

 I am very new to DTI analysis and also DSI studio. I am planning to analyze DTI in macaques. Is it possible to be able to do auto tracking for macaques similar to HCP1065 template? Here is the template for macaques https://www.nitrc.org/projects/rmdtitemplate/

Thank you so much,

Yasaman

[Frank Yeh]

Yes, it is possible, but I haven't tried it yet. Do you have a FIB
file that can share? I will test it on DSI Studio and make sure it
works for you.
Best,
Frank

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[yasaman bagherzadeh]

Thank you for your prompt response! Do you mean FIB file of my data or FIB file of atlas? (Sorry if this is a dumb question, I am very new in the field). 

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[Frank Yeh]

No problem. I was not clear enough.
I meant the FIB file of your sample data.
Frank

On Wed, Jun 2, 2021 at 7:58 PM yasaman bagherzadeh

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[Frank Yeh]

This discussion forum is public, and anyone can download the data. Is this okay?
(If not, I can remove this thread) I already downloaded the data.
Frank

On Wed, Jun 2, 2021 at 8:20 PM yasaman bagherzadeh
<yass.bag...@gmail.com> wrote:
>
> Thank you! I attached the FIB file.

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[Frank Yeh]

I checked the data, I may need the SRC file to rotate the image
volume. You can send it using the link provided on the top banner of
the discussion forum.
Frank

[yasaman bagherzadeh]

Is it possible that I share it by email?

[Frank Yeh]

You can use the private link:
https://www.dropbox.com/request/W0hJkAIVC2keWAjqtqvU
Frank

On Wed, Jun 2, 2021 at 9:29 PM yasaman bagherzadeh
<yass.bag...@gmail.com> wrote:
>
> Yes, please remove the thread, and how I can send the SRC to you?
> Thank you!

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[yasaman bagherzadeh]

done!

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[Frank Yeh]

Thanks! I got the data.

Do you mind if I create a publicly available video showing how to
troubleshoot this dataset and generate automatic fiber tracking?
The purpose is only to help other people who shared the same question.
No SRC or FIB will be shared.
It is entirely okay if you have a concern, and I can send you a list
of steps I have used.

Please feel free to let me know.

Best,
Frank

On Wed, Jun 2, 2021 at 9:50 PM yasaman bagherzadeh

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[yasaman bagherzadeh]

Sure, I don't mind. Please do that!

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[Frank Yeh]

Much appreciated. I will record a video and send the link to it.
Anyone I can put on the acknowledgement besides you?
Frank

On Wed, Jun 2, 2021 at 10:15 PM yasaman bagherzadeh

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[yasaman bagherzadeh]

Thank you, Frank! Please mention "Jitendra Sharma" as well.

Yasaman

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[Frank Yeh]

Hi Yasaman,

    I created a video to show how to run automatic tracking for your data.

    Hope this helps: https://www.youtube.com/watch?v=XHk_gQN72rU

Best,

Frank

[yasaman bagherzadeh]

Thank you very much Frank for the video instructions. It was very helpful. Just one question. After I swap and flip the image in Y and Z direction, do I need to flip the b table as well?

Thank you!

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[Frank Yeh]

You don't have to because the b-table will also be swapped/flipped accordingly.
Also, the [check b-table] function will further test different
orientations and choose the best one.

Glad to know that the video helps.
Best,
Frank

On Thu, Jun 3, 2021 at 2:30 PM yasaman bagherzadeh

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