Fiber tracking in newborns

[Océane-Rose Leloutre-Salat]

Dear Fang-Cheng Yeh,

I hope this message finds you well.

I am currently involved in a research project that takes part in the analysis of newborn MRI scans. Our project consists of evaluating the impact of brain disruptors. 

We are looking at the connectivity of the prefrontal cortex, the amygdala and the hippocampus. We are encountering challenges in effectively using DSI_Studio. Our main issue stems from working with infant MRIs on an adult MRIs template, such as the HCP842 Population-Averaged Tractography Atlas. We read the methods of a previous paper using this technic on children’s MRIs :

Graziano PA, Garic D, Dick AS. Individual differences in white matter of the uncinate fasciculus and inferior fronto‐occipital fasciculus: possible early biomarkers for callous‐unemotional behaviors in young children with disruptive behavior problems. Child Psychology Psychiatry. janv 2022;63(1):19‑33.

Our goal would consist of creating a new template with baby MRIs from the dHCP or our own data and to transpose it on the HCP842 altas. We would then use this new template on our MRIs data to auto track the fibers we need. We wish to use the auto tracking fibers accordingly on baby datas.

Given your experience in this area, could you assist us in overcoming these obstacles and optimizing our use of DSI_Studio for our specific needs.

Would it be possible to schedule a meeting  to discuss our project in detail? We would greatly appreciate your time and expertise.

Looking forward to your response.

Best regards,

Océane-Rose

[Frank Yeh]

Could you post a screenshot of whole brain tracking of your infant data, and see if the tracts look good? 

This may help rule out the cause of the issue.

Frank

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[Océane-Rose Leloutre-Salat]

Hi, 

Thank you for your fast answer. Here are the screenshots of the whole brain tracking. 

Thank you !

[Océane-Rose Leloutre-Salat]

Hi Frank, thank you for your fast answer. Here are the screenshots of our whole brain tracking.

Océane-Rose

Le mardi 11 juin 2024 à 15 h 14 min 55 s UTC-4, Frank Yeh a écrit :

[Ophelia Dalkiriadis]

Hi Frank, 

 Thank you for the quick answer. I am on the same research team as Océane-Rose. Here are some pictures of the fiber tracking.

Best regards,

Ophelia

[Frank Yeh]

The tractography quality looks okay.

You may switch the template to "ICBM152 adult" at Step T3a Assign Regions and use Autotrack to make pathways.

You may also need to change the min length, max length and tolerance at Step T3c tracking parameters to get the best results.

Best regards,

Frank

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[Océane-Rose Leloutre-Salat]

Hi Frank, 

Thank you very much for your assistance. 

Here is what the autotracking of the uncinate fasciculus provides us when we use the template ICBM152 adult (without changing the min length, max length and tolerance):

We were thinking about using ANTs to process our infants data. Our goal would be to implant a new template (neonatal) to DSI_studio. Our problem reside in creating and understanding the content of the tt.gz files needed for the tractography. We wish to create a template within the same range as yours. 

Could you give us more insight on how to proceed or on who we need to contact ?

Best, 

Océane-Rose

[Frank Yeh]

I am not familiar with ANTs, and perhaps you may check out ANTs documentation or their team to see if there is a solution?

Best regards,

Frank

[Océane-Rose Leloutre-Salat]

When you created the templates, how did you generate the tt.gz files for the tracking ?

Océane-Rose

[Frank Yeh]

tt.gz is generated from fiber tracking, but the other way around.

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[Océane-Rose Leloutre-Salat]

When we create a template, do we need a specific file for the tracking to work and generate this tt.gz  ?

[Frank Yeh]

Yes, you may check out tutorial videos at wk2 and wk3 at https://practicum.labsolver.org/

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