How to add new tract template/atlas in Autotracking?

[yh]

Dear professor Yeh:

    Thank you for devoloped DSIstudio which is a really a powerful tool help me study my project. My trouble is that I want to track fibers not exist in the autotracking list such as Potine-cereberum fibers and Olivocerebellar tract in 30 patients an 30 health control. To ensure the consistence of tracking progress, i think autotracking  is the best choice in stepT3d, but I can't find tract name in the list. 

   So far, i can tracking these fibers by manually drawing ROI in stepT3a and run Fibertracking in stepT3d and then edit the tract/fibers according to your teaching vedio for a specific subject. But for 60 subjects, I think it is not sensible.

   I havd searched the google "how to add new tract/  how to add new tract template " and search the disscusion group with key word "tract" still can't find solution. In addition I searched  your twitter,  MRIIT twitter you reposted has tract template seems to mostly the same tract as your autotracking name list. 

   I am a neurosurgeon in my second year of dcotor degree. In my study I want to compare tracts(mentioned above,which seems to related to language related in previous study report) differences between  patient group and health control group. 

Best wishes 

hope to see your reply.

[Frank Yeh]

Hope this helps:
http://dsi-studio.labsolver.org/Manual/automatic-fiber-tracking#TOC-Optional-Add-New-Tracts

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[yh]

Professor Yeh

   Thanks to your reply, it works very well.

   But i have encountered another big question, how to keep the track that I added to the existing tractography atlas as good/percise as you havd strored in the software. In other word, may i know how you made the tractgraph atlas(those tract in the autotrack list). 

   I have read the tutorial about autotrack function and the cited paper ([5] Yeh, F. C., Panesar, S., Barrios, J., Fernandes, D., Abhinav, K., Meola, A., & Fernandez-Miranda, J. C. (2018). Improved Accuracy of Diffusion MRI Tractography Using Topology-Informed Pruning (TIP). Neurotherapeutics .). I can't find out how you tracking these fibers out and save them as tractography atlas, 

   Could you please tell me where i can get related information or may I have a related paper about how the tractography atlas was made. I do really want to add some other tracts to the list and want follow your protocal. In another word, if I can reproduce you tract template, it proves that I make a good tract template for other tract not listed in the autotracking list.

   Best wishes
   Hope to see your reply

在 2021年1月11日星期一 UTC+8下午12:27:17，Frank Yeh写道：

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[Frank Yeh]

Hope this helps: https://pubmed.ncbi.nlm.nih.gov/29758339/

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[yh]

Hi Frank,

    I have read the paper you recommened carefully and try to surmmarize the steps to produce the tract atlas used in the autotracking as below:

      1 Geting data from HCP;

      2 Using QSDR method and resgistrate to FSL FA space;

      3 Generate average SDF template,voxel by voxel;

      4 Whole brain fiber tracking, 10k streamline every angular value will produce and all 50k streamlines were clustered. 550 cluster was generated;

      5 Labeling cluster according anatomical knowledge, cluster with same name grouped together to from major fiber bundles. Then additional missing fiber (cant find details) was checked.

 

    I’d like to repeat these steps but constrained by lacking cluster related knowledge and labeling is really time consumig. So, If possible, could you please share the labeled 550 cluster file that containing more tracks addition to those tract in the autotrack list? After that, I can group cluster into tract that I want to study.

Best regards,

Hu Yin

在 2021年2月9日星期二 UTC+8下午10:28:54，Frank Yeh写道：

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[Frank Yeh]

Sure. I will upload the data and get back to you then.
Frank

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[yh]

Hi Frank,

   So happy to receiving the good news from you, thank you for your generosity. I will check this website everyday, Thank you!

 

Best regards,

Hu Yin

Department of Neurosurgery, Beijng Tiantan Hospital, Capital Medical University.

No.119, South 4th Ring Road West. Fengtai District, Beijing, China.

Tel: 18810252625

E-mail: huyi...@hotmail.com,

在 2021年3月4日星期四 UTC+8下午10:14:31，Frank Yeh写道：

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[Frank Yeh]

The 550 clusters are here: https://pitt.box.com/s/4muwbvbi9fq7upzlqntr36neosnxl797

The labels: https://pitt.box.com/s/btbcf1dbd7kqv77ux3n9sptkahjn50pg

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[yh]

Hi Frank,

I have down loaded the 550 trk file and 10 lable file from the linkage that you posted in your reply. There are still some questions that I hope to get answer from you;

Q1: May I take <Clusters_2nd_edition.xlsx> as final version of the lable file? Bacause it seems that all clusters not belong to those major tracks was classified as “false track”.

Q2: Should I take the “false track” (with mark “F”) as unclassified (into major tracks) track?  I think it is definitely more tracts exist in nervous system than all the tract you have mentioned in you paper, so I hope you could help me to confirm this.

Best regards,

Hu Yin

Department of Neurosurgery, Beijng Tiantan Hospital, Capital Medical University.

No.119, South 4th Ring Road West. Fengtai District, Beijing, China.

Tel: 18810252625

E-mail: huyi...@hotmail.com

在 2021年3月11日星期四 UTC+8上午8:38:57，Frank Yeh写道：

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[Frank Yeh]

>
> I have down loaded the 550 trk file and 10 lable file from the linkage that you posted in your reply. There are still some questions that I hope to get answer from you;
> Q1: May I take <Clusters_2nd_edition.xlsx> as final version of the lable file? Bacause it seems that all clusters not belong to those major tracks was classified as “false track”.

It is not the final, because there is a further team discussion that
led to minor modifications. The final result is the atlas we released.

> Q2: Should I take the “false track” (with mark “F”) as unclassified (into major tracks) track? I think it is definitely more tracts exist in nervous system than all the tract you have mentioned in you paper, so I hope you could help me to confirm this.

No, they are false tracks. Some missing tracks are tracked separately,
as mentioned in tha paper.

Best regards,
Frank

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[natan derek]

Hi,

Is there any follow-up after this? I am curious since I am also planning to create our own atlas instead of using HCP-842 since our subjects are old people.

Best wishes, 

Natan

[Frank Yeh]

All follow-up studies are shared at https://brain.labsolver.org/hcp_trk_atlas.html

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[natan derek]

Thank you so much for the prompt reply. I'm just curious if the HCP atlas created from young adults can be used also for the old people in our case ?

[Frank Yeh]

It depends on the application, but in most cases should be good.

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