Approaches to integrate PAM50 to human ex-vivo multi-contrast templates

MRI Processing
1

Dear Spinal Cord Developers Team,

I have generated below Ex-vivo human multi-contrast templates using T1, b0 and FA using antsMultivariateTemplateConstruction.sh. approach. These templates are covering the cervical level from C3-C7.

Please note that all the pre-processing steps were done using your SCT and your invaluable feedback, help, and support EXCEPT template construction.

multi_modal_template
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My aim is to integrate these templates to PAM50 template/Atlas (or the opposite way), What is the right approach in my case?

Also, I wonder what is the best approaches or specific pipelines to handle these registration between in-vivo template and ex-vivo template. I looked at most of the courses which illustrating registration between PAM50 to in-vivo data.

Could you please advice if there is a specific pipeline for this form of integration?

Please let me know if further information is needed to help sorting this out.

Many thanks in advance for your continuing support and cooperation.

Cheers,

Ibrahim

2

Hi @ihattan,

This is great work! As for integrating it with the PAM50 template, this is not trivial.

We have a precedent of a high resolution histology dataset having been aligned with the PAM50 physical space coordinate. More detailed in this PR.

We also have current efforts to bring high resolution templates to the PAM50:

I encourage you to first look at the various initiatives, to make sure there is no duplicated work (eg: how does your template compare to GitHub - spinalcordtoolbox/exvivo-template: High resolution ex-vivo MRI template of the cervical spinal cord.), and then propose actions moving forward. As you know, a benefit of the template is to have access to a white/gray matter atlas, for atlas-based quantification of qMRI metrics. This is also something that you might need to implement if you wish to move forward with PAM50 integration. But this raises questions of how to identify the atlas (see the related issues/PRs on the links above, we discuss this).

Cheers
Julien

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This is great work! As for integrating it with the PAM50 template, this is not trivial.

Thank you for your response, Julien and I agree it would be challenging after I went through the PRs issues. However, I would greatly appreciate any insights you could share regarding effective methodologies for creating high-quality anatomical and diffusion atlases. I am hopeful that our work together may result in an insightful and fresh atlas that considerably increases our understanding of the cervical spinal cord and its therapeutic consequences. This aspect would be available for any collaboration from any team to work together.

We have a precedent of a high resolution histology dataset having been aligned with the PAM50 physical space coordinate. More detailed in this PR .

We also have current efforts to bring high resolution templates to the PAM50:

I encourage you to first look at the various initiatives, to make sure there is no duplicated work (eg: how does your template compare to GitHub - spinalcordtoolbox/exvivo-template: High resolution ex-vivo MRI template of the cervical spinal cord. ),

The current SCT T1 ex-vivo template combines data from 13 subjects, including 5 normal coherent and 8 prefix coherent in one anatomical template. However, my work will be based on creating 2 anatomical templates, one for the normal coherent and the other one for the prefix coherent. In addition, my work aims to incorporate diffusion MRI with the traditional anatomical imaging for each group (normal and prefix cervical cord).

and then propose actions moving forward. As you know, a benefit of the template is to have access to a white/gray matter atlas, for atlas-based quantification of qMRI metrics. This is also something that you might need to implement if you wish to move forward with PAM50 integration. But this raises questions of how to identify the atlas (see the related issues/PRs on the links above, we discuss this)

I would be very interested to learn about any successful approaches or techniques you have used when developing atlases, especially with reference to the incorporation of multi-contrast data.

At this stage, I will be focusing on registering my templates to the PAM50 template instead of physically aligning them, with the main goal being to use the current PAM50 atlas for diffusion MRI analysis. In regard to this approach, I’m in need of feedback on whether a specific pipeline or standard pipeline in your SCT course will work in my case. Also, what is the best atlas to use in the meantime for my analysis within SCT atlases that are available from your point of view?

Thank you once again to you and your team for the invaluable feedback and ongoing support for SCT users.

Cheers,

Ibrahim

4

Great! If you have specific questions about your investigations please feel free to post–

Cheers,
Julien

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5

Thank you Julien for your response. My specific questions are above.i know you are busy, so whenever you have a chance, please share your insight about my investigation mentioned above please.
.

Cheers,

Ibrahim

6

Hi Ibrahim.

These questions are too broad and difficult to answer.

Eg:

I’m in need of feedback on whether a specific pipeline or standard pipeline in your SCT course will work in my case

I would need to understand all the details of your data and analysis pipeline you are planning to use, so I cannot give you constructive feedback. Generally speaking, whatever you need to do and can do on the PAM50 template, will require the same template/atlas objects for your new template/atlas. Eg: if you wish to extract qMRI metrics within a specific tract, then that tract needs to be defined in the atlas/ folder to be used with sct_extract_metric.

what is the best atlas to use in the meantime for my analysis within SCT atlases that are available from your point of view?

The PAM50 template.

1 Like