Whole-Brain Tractography Processing Questions

[Jessica Hua]

Hi DSI Studio,

I had some questions about the tractograpy implemented in DSI Studio. 

For the tractography step, these were my parameters: A DTI diffusion scheme was used, and a total of 30 diffusion sampling directions were acquired. The b-value was 800 s/mm2. The in-plane resolution was 2 mm. The slice thickness was 2 mm. The b-table was checked by an automatic quality control routine to ensure its accuracy (Schilling et al. MRI, 2019) . The diffusion tensor was calculated. A deterministic fiber tracking algorithm (Yeh et al., PLoS ONE 8(11): e80713, 2013) was used. A seeding region was placed at whole brain. The anisotropy threshold was 0.1. The angular threshold was 45 degrees. The step size was randomly selected from 0.5 voxel to 1.5 voxels. Tracks with length shorter than 30 or longer than 300 mm were discarded. A total of 50000 seeds were placed.

1) Is there a way to set a certain number of seeds at each voxel (e.g., 8 seeds at each voxel)? 

2) Is there an advantage of setting a seed at subvoxel vs. voxel? 

3) I want to terminate a streamline if a streamline makes a sharp turn > 45 degrees. By setting the angular threshold to 45 degrees, am I accomplishing that?

4) I selected to check ending. Is there a rationale to not check the ending? 

5) And in the setup I currently have, can streamlines exceed the brain mask? 

Thanks for your help!

Jessica

[Fang-Cheng Yeh]

1) Is there a way to set a certain number of seeds at each voxel (e.g., 8 seeds at each voxel)? 

You may specify a seed file as what is described here: http://dsi-studio.labsolver.org/Manual/Fiber-Tracking#TOC-Seed

2) Is there an advantage of setting a seed at subvoxel vs. voxel? 

Tractography has the potential to achieve super-resolution

 

3) I want to terminate a streamline if a streamline makes a sharp turn > 45 degrees. By setting the angular threshold to 45 degrees, am I accomplishing that?

Yes. 

4) I selected to check ending. Is there a rationale to not check the ending? 

Yes, check ending use anisotropy to check the termination. If a track is terminated by the angular threshold, the whole track will be discarded. 

5) And in the setup I currently have, can streamlines exceed the brain mask?  

 A track can exceed the brain mask by a step and stop just right outside the mask edge.

Best,

Frank

Thanks for your help!

Jessica

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[Gauthami Nair]

Hello Sir,

I have another question with regard to interpreting the results I get after putting age and group as covariates in group Connectometry analysis.

My doubt is that the report states 82% decreased connectivity with regard to age but how do I interpret whether this is in the patient or control group?

Even when I added group as a variable ( Control 1 and patient 0), I got 85% decreased connectivity but I am still not able to identify whether it is in the patient or control group.

I am also attaching the report I got for the same analysis. 

Thank you very much for your help sir.

Sincerely,

Gauthami

[Fang-Cheng Yeh]

Here the (82%) is the percentage of the total findings. It is not
the percentage of decreased connectivity.
Frank

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[Gauthami Nair]

So I have two other questions regarding this -

1) is it possible to find out increased or decreased connectivity in patient group vs. control?

2) also if 82% is the total findings what exactly can I infer or understand from that report?

Thank you

Sincerely,

Gauthami

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[Fang-Cheng Yeh]

> 1) is it possible to find out increased or decreased connectivity in patient group vs. control?

http://dsi-studio.labsolver.org/Manual/diffusion-mri-connectometry#TOC-Scatter-plots

> 2) also if 82% is the total findings what exactly can I infer or understand from that report?

corpus callosum (82%) here means 82% of the total finding are located
at corpus callosum.
The percentage may not be meaningful, and it will be replaced in the
near future to avoid confusion.
Frank

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