problems with alignment and WHS atlas

[José Michelle Doeren]

Dear Frank,

First of all, thank you very much for providing DSI-Studio and for being so available to answer questions and engage with users – this is incredibly motivating for young researchers like myself!

We are currently working on analyzing rat brain data using DSI-Studio and have encountered a few issues. I would greatly appreciate any guidance or advice you could offer.

1. We are experiencing some challenges with the manual alignment of our data, which seems similar to a question raised by Khan Hekmatyar (20.01.2024, on this forum). Specifically, our coronal sections end up aligned as sagittal sections if we apply "flip YZ" . If helpful, I can provide a screenshot to illustrate the issue more clearly 😊.

2. When using the DUKE Atlas for rat brains, it appears that the “VTA_Ventral_Tegmental_Area” is missing from the application. Although we can select all other areas and retrieve statistics, there are no values available for the VTA (left and right). I think it is a problem with the implementation of the atlas in DSI.. Do you have any idea on how we might resolve this?

3. We also noticed that the WHS atlas is mentioned as the default for rat brains in DSI-Studio (according to https://www.nature.com/articles/s41592-023-02034-3, for SD rats), but the DUKE atlas <(for Wistar Rats) is the only option available in the software for rat brain analysis (in contrast to multiple atlas options for mice and human brains). In the DSI-Studio folders, I only found label information for the DUKE atlas. Would it be possible to include the WHS atlas and its labels (available here: https://www.nitrc.org/projects/whs-sd-atlas/)? We tried adding it ourselves but were unsuccessful.
   
   On the same note, if feasible, additional atlas options for rat brains in DSI-Studio would be of immense benefit to researchers working with various strains and regions of interest. I understand that implementing new atlases may involve considerable time and effort..  If it’s something you might consider for the future, here are a few atlases that could be especially useful:
   
   Sigma Atlas for Wistar Rat (https://www.nitrc.org/projects/sigma_template)
   
   Calabrése Atlas (for developing rat brain, with an additional segmentation of 26 regions for the adult p80 brain) – available at https://www.civm.duhs.duke.edu/duke-CIVM-sup-2013diffratbrain. I have downloaded this data and would be more than willing to share it with you for possible implementation if it helps.
   
   Paxinos-Based White Matter Tract Atlas for Sprague Dawley rats (https://www.sciencedirect.com/science/article/pii/S0730725X17301364?via%3Dihub)
   
   Tohoku Atlas for Wistar Rats (https://www.frontiersin.org/journals/neuroinformatics/articles/10.3389/fninf.2011.00026/full)

   
   

Thank you very much for your time and consideration! We would be grateful for any assistance or insights you could provide to address these questions and suggestions.

Best regards,
José

[Frank Yeh]

1) Screenshot will be helpful. If there is a sample dataset, I can
check to see if there is a problem.
2) I checked the atlas. VTA is very small, and even under the
template, it is only two voxels. If your data does not have a high
resolution, VTA is unlikely to be visible.
3) Thanks for providing the list. I will have this on the task queue
to get those available.

Best,
Frank

> --
> 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-studio+...@googlegroups.com.
> To view this discussion visit https://groups.google.com/d/msgid/dsi-studio/16f24d7b-c642-488f-8f99-c740e627886bn%40googlegroups.com.

[Yuliya K]

Dear Frank, 

Thank you for your help! We work together with Jose and I will send you now two examples. We have acquired data with the slice thickness of 1 mm and also 0.6 mm. I will send you both. 

Thank you. 

Yuliya 

четверг, 14 ноября 2024 г. в 19:29:39 UTC+1, Frank Yeh:

[José Michelle Doeren]

Dear Frank, 

As mentioned above, my colleague provided 2 of our example data via the dropbox-link you attached to this google group.
I provide now a screenshot of what the problem with our alignment is after "T2 Reconstruction"

The workflow we follow is: 

- adjusting treshold + erase background

-apply motion correction

-apply volume correction

-flip Y (in order to correct image orientation, as described in T2 on your website https://dsi-studio.labsolver.org/doc/gui_t2.html)

- check b table (what is the difference between “check b-table” and “check b-table template-based" ?)

-  when asked “this seems to be an animal scan in non-axial orientation. Correct image orientation?" We say “yes”

 

1.      We end up with it being upside down and (more importantly) the wrong orientation of the atlas (mixed anterior and posterior; see the image I provided for the example of corpus callosum)

Thank you very much for your help!
Best regards,
José

[Frank Yeh]

Thank you for sending the data, and I examined it.

There is a bug in DSI Studio when flipping/swapping image volume. The voxel size won't update, and cause errors (very sorry about it). 

I updated DSI Studio, and today's version should provide correct results.

Using the updated version, I found the steps to reconstruct the data:

(1) Click [Step T2][Reconstruction] open 2dseq.sz
(2) At the top menu, select [Step T2][Corrections][EDDY]   (You may replace this with [Motion Correction])
(3) At the top menu, select [Step T2][Edit][Image swap yz]
(4) At the top menu, select [Step T2][Edit][Image flip x]
(5) At the top menu, select [Step T2][B-table][Check B-table2]
(6) Set [Step T2b(1)]=GQI     (The updated version won't ask to correct orientation because the bug is fixed, and the image looks correct now)
(7) Set [Step T2b(1)][Diffusion sampling length ratio]=0.6
(8) Click [Step T2b][Run reconstruction]

Loading the FIB file, and I can use the atlas function:

SNR is good, but fiber tracking won't work here because the image does not have enough "diffusion attenuation" or diffusion contrast. You may see the anisotropy map is not good due to this.

Increasing diffusion time or diffusion encoding duration may improve it.

If you have further questions, please feel free to let me know.

Best,

Frank

To view this discussion visit https://groups.google.com/d/msgid/dsi-studio/a84abd60-cd75-4bb1-846c-6ea1b57b1652n%40googlegroups.com.

[Yuliya K]

Thank you very much, Frank! You have checked everything faster than we downloaded the second set :) Please, don't be surprised to get it. 

I will download the new version and follow yours steps (thank you very much! it is so helpful) . Hopefully, it works!  

пятница, 15 ноября 2024 г. в 16:27:32 UTC+1, Frank Yeh:

[Frank Yeh]

I updated DSI Studio again to fix another bug that does not generate tractography. 

If you just downloaded DSI Studio, please update it again.

(Sorry for the hassle)

Frank

[José Michelle Doeren]

Dear Frank, 

I hope this message finds you well. While working on our data, some new questions came up:

- could you give a brief explanation whether there is a relationship between the b-value and the Diffusion sample length ratio (DSLR)? You recommended a DSLR of 0.6 for our data with a b-value of 650, would we need to adjust this for data b-value1000?

- i wanted to ask for your professional opinion on interpreting FA/QA abnormalities in gray matter structures? Is there any literature (or youtube clip) you recommend? To me it seems like the DTI-community holds many opinios..

lastly, I wanted to catch up whether you may be able to indicate when new rat atlas could be available on DSI?

thank you very much for your help
have a merry christmas!

[Frank Yeh]

> - could you give a brief explanation whether there is a relationship between the b-value and the Diffusion sample length ratio (DSLR)? You recommended a DSLR of 0.6 for our data with a b-value of 650, would we need to adjust this for data b-value1000?

The ideal value depends on many acquisition factors, and I would just
try different settings and see which the results look the best.

>
> - i wanted to ask for your professional opinion on interpreting FA/QA abnormalities in gray matter structures? Is there any literature (or youtube clip) you recommend? To me it seems like the DTI-community holds many opinios..

For in-vivo studies, you may check out
https://practicum.labsolver.org/metrics.html and its tutorial videos.
For ex-vivo studies, interpretation is much harder because the
fixation changes many things. There won't be a simple interpretation

>
> lastly, I wanted to catch up whether you may be able to indicate when new rat atlas could be available on DSI?

We are still working on it, and it may take a long time.
I would suggest you install an atlas you would like to use in DSI
Studio so that there won't be a delay due to our progress.

Best,
Frank

>
> thank you very much for your help
> have a merry christmas!
>
> Frank Yeh schrieb am Freitag, 15. November 2024 um 17:57:27 UTC+1:
>>
>> I updated DSI Studio again to fix another bug that does not generate tractography.
>> If you just downloaded DSI Studio, please update it again.
>> (Sorry for the hassle)
>> Frank
>

> --
> 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-studio+...@googlegroups.com.

> To view this discussion visit https://groups.google.com/d/msgid/dsi-studio/7fb96b6f-1233-4608-8f3a-76ac31c29321n%40googlegroups.com.