how to specify seed density

[Vinny]

Hi,

Is there a way to specify seed density (for example, 1 or 5) for tractography in the DSI Studio GUI?  I'd like to replicate published tracking parameters for corticospinal tracts.  I am using the dsi_studio_ubuntu_2004 package.  I've attached a screenshot of the tracking parameters.

Thanks,

Vinny

[Frank Yeh]

1. Use the Step T3a atlas to load CST from the built in tractography atlas as a region

2. Top menu - Regions - Statistics to get the voxels count

3. Multiply voxels count with the density to get the tract count

4 Specify tract count in the tracking parameter.

--
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/bd842ed7-d50e-4b49-9003-b8b0d9f0e75cn%40googlegroups.com.

[Vinny]

Thank you for the guidance, I was able to reconstruct the CST using the tract count from Steps 1-4 and manual ROIs.  I find that using the default DSI Studio parameters (ie, terminating if there are 1000000 seeds) resulted in more tracts than specifying tract count (from seed density of 1), but the fiber distribution was very similar. 

However, for replicating what has been done in the literature for tractography where manual seed and end regions are delineated, a seed density of 1 is used, and I am assuming that seed density is referring to the seed region itself.  My seed region for the corticospinal tract is 87 voxels so I specified to terminate if there are 87 seeds?  In this case, I get 17 fibers (as opposed to 8641 fibers based on tract count, or 152594 fibers based on default DSI Studio parameter).  Was this a correct implementation of seed density (for the seed region only) in DSI Studio?

Thanks,

Vinny

[Frank Yeh]

> However, for replicating what has been done in the literature for tractography where manual seed and end regions are delineated, a seed density of 1 is used, and I am assuming that seed density is referring to the seed region itself. My seed region for the corticospinal tract is 87 voxels so I specified to terminate if there are 87 seeds?

It seems that you are using a different dataset, and it is unlikely
that the tractography can be reproduced.

The optimal setting will be largely different, and you may check out
tutorial videos at practicum.labsolver.org to figure out how to find
the best setting.

Best,
Frank

>
> Thanks,
>
> Vinny
>
> On Friday, January 10, 2025 at 9:56:35 PM UTC-5 Frank Yeh wrote:
>>
>> 1. Use the Step T3a atlas to load CST from the built in tractography atlas as a region
>> 2. Top menu - Regions - Statistics to get the voxels count
>> 3. Multiply voxels count with the density to get the tract count
>> 4 Specify tract count in the tracking parameter.
>>
>>
>>> Hi,
>>>
>>> Is there a way to specify seed density (for example, 1 or 5) for tractography in the DSI Studio GUI? I'd like to replicate published tracking parameters for corticospinal tracts. I am using the dsi_studio_ubuntu_2004 package. I've attached a screenshot of the tracking parameters.
>>>
>>> Thanks,
>>>
>>> Vinny
>>>
>>> --
>>> 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/bd842ed7-d50e-4b49-9003-b8b0d9f0e75cn%40googlegroups.com.
>
> --
> 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/c4310bdf-9d7a-46fb-9347-fca9b9b8d715n%40googlegroups.com.