Tractography Methods and Template/Atlas Registration for Neonates

[Maryam Shapourjani]

Hello Dear Frank,

I have three questions:

First: Before using DSI Studio software, I linearly registered the brain images of the **neonates** I have onto a **neonate** template. Then I used DSI Studio software (Generalized Q-Sampling Imaging (GQI) method) and performed tractography in the next step. Is it problematic that I used a template and performed registration **before** using the software?

Second: After registering the image onto the **neonate** template and then using DSI Studio software (GQI method), I used an **adult** tractography atlas in the tractography step. Does an adult tractography atlas get registered onto the neonate brain at this stage (the tractography stage)?

Third: If the answer to the second question is positive, based on the work I have done, it seems I have performed two registration steps: once, before using DSI Studio software, I linearly registered the subjects onto a neonate template, and a second time in the tractography step by using an adult tractography atlas. In this case, I have performed registration twice, which would cause an error.
What is your opinion on this matter? I would be grateful if you could guide me.

Sincerely,
Maryam Shapourjani

[Frank Yeh]

Sorry for my delayed reply:

> First: Before using DSI Studio software, I linearly registered the brain images of the **neonates** I have onto a **neonate** template. Then I used DSI Studio software (Generalized Q-Sampling Imaging (GQI) method) and performed tractography in the next step. Is it problematic that I used a template and performed registration **before** using the software?

Yes, it may have an orientation issue because the b-table has to be
rotated by the jacobian matrix of the registration.
I would use QSDR reconstruction to get data into the neonate template space.

>
> Second: After registering the image onto the **neonate** template and then using DSI Studio software (GQI method), I used an **adult** tractography atlas in the tractography step. Does an adult tractography atlas get registered onto the neonate brain at this stage (the tractography stage)?

This should be fine if the first step's issue is corrected.

>
> Third: If the answer to the second question is positive, based on the work I have done, it seems I have performed two registration steps: once, before using DSI Studio software, I linearly registered the subjects onto a neonate template, and a second time in the tractography step by using an adult tractography atlas. In this case, I have performed registration twice, which would cause an error.
> What is your opinion on this matter? I would be grateful if you could guide me.

One is linear registration and another is nonlinear registration. They
complement to each other.

Best regards,
Frank


>
> Sincerely,
> Maryam Shapourjani
>
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