Other atlases for mice

[adam....@gmail.com]

Hi Frank,

I have a question: Is there a way to import other atlases based on T2 structural images for mice (e.g., the DSURQE atlas from http://repo.mouseimaging.ca/repo/DSURQE_40micron_nifti/)?

[Frank Yeh]

It is possible.
I will check them out and get back to you.

On Wed, Feb 3, 2021 at 1:43 PM <adam....@gmail.com> wrote:
>
> Hi Frank,
>
> I have a question: Is there a way to import other atlases based on T2 structural images for mice (e.g., the DSURQE atlas from http://repo.mouseimaging.ca/repo/DSURQE_40micron_nifti/)?
>

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[Frank Yeh]

You may update DSI Studio (dated today) and the atlas is included.
Best,
Frank

On Wed, Feb 3, 2021 at 1:43 PM <adam....@gmail.com> wrote:
>

> Hi Frank,
>
> I have a question: Is there a way to import other atlases based on T2 structural images for mice (e.g., the DSURQE atlas from http://repo.mouseimaging.ca/repo/DSURQE_40micron_nifti/)?
>

[Adam Raikes]

Sounds good. I'll check it out today.

Would you be willing to walk me through what you needed to do so that I can locally use other mouse atlases (Dorr, AMBA, etc) rather than always needing you to update the software (I recognize that's time out of your day to address something I reasonably I could probably do on my end).

On Wednesday, February 3, 2021 at 8:07:38 PM UTC-7, Frank Yeh wrote:

You may update DSI Studio (dated today) and the atlas is included.
Best,
Frank

On Wed, Feb 3, 2021 at 1:43 PM <adam....@gmail.com> wrote:
>
> Hi Frank,
>
> I have a question: Is there a way to import other atlases based on T2 structural images for mice (e.g., the DSURQE atlas from http://repo.mouseimaging.ca/repo/DSURQE_40micron_nifti/)?
>
> --
> 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-s...@googlegroups.com.

[Frank Yeh]

For this atlas, I first masked the background in atlas's average using the
atlas's mask using O4.
Then I got the edge image from the atlas label in O4 and also the edge
image of CIVM QA for further edge-based nonlinear registration.
Then, I wrapped atlas's edge image to that of the CIVM QA at O7
nonlinear registration, with the masked atlas image and CIVM ISO added
as additional volume to help normalization. The smoothing is increased
to 0.6. Once done, I applied the wrapping to the original label image.

I also applied several rounds of smoothing in O4 to the atlas label image
before all these steps because the boundary is not smooth.

Wish I can provide a standard tutorial, but the same strategy may not
work for other atlases. I usually try different approaches and
evaluate which is the best, and sometimes I have to modify DSI Studio
and open up new functions to enable certain features.



Frank

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[adam....@gmail.com]

Understood. 

I used the download link for Windows and it still has the 2021-01-11 release.

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[Frank Yeh]

You may try other links.
Frank

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[adam....@gmail.com]

That worked.

Do you mind if I send you one other atlas on dropbox then?

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[Frank Yeh]

You are welcome to send me at any time.
Frank

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[adam....@gmail.com]

I uploaded the Dorr 2008 atlas (including template brain, label file, and label mappings).

Thanks as always.

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[Frank Yeh]

Thanks! I will check them out.
Frank

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[Frank Yeh]

Dorr atlas is included (today's Windows version).
If you are using Mac or Linux version, please let me know. I will
commit the update for them.
Frank

[Zuo Wang]

Hello;  I am a neuroscience researcher currently working on mouse brain MRI analysis and I would like to request access to the Dorr 2008 mouse brain atlas dataset, I can not download from website:

Dorr AE, Lerch JP, Spring S, Kabani N, Henkelman RM. High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice. NeuroImage. 2008;42(1):60–69.

Specifically, I am seeking the following components:

- The T2-weighted average brain template (`.nii.gz`)
- The corresponding labeled segmentation file
- The label mapping table (structure names and index values)

I have experienced difficulty accessing the original hosting URL (repo.mouseimaging.ca) and would greatly appreciate an alternative download link, or a direct email copy if possible.

This dataset will be used solely for academic and non-commercial research purposes. Proper citation and attribution will be ensured.

Thank you very much for your time and assistance. I look forward to your response.

[Frank Yeh]

Thank you for the suggestion.
I am listing this on the to-do list.

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