Troubleshooting disconnected networks

[Alexa Mousley]

Hi Frank,

I'm using the Fiber Data Hub for a project with ABCD. I'm using the .fib files to track with the Brainnetome Atlas but unfortunately when I track them, most of the networks I'm getting are not fully connect - as many as 20 separate components. I still have this issue when I use other atlases. I'd love to stick with DSI Studio but I'm not sure if it's possible to get fully connected network - which is essential for my project. Here are my tracking parameters:

dsi_studio --action=trk --connectivity=Brainnectome --turning_angle=35 --step_size=1.0 --min_length=30 --max_length=250 --connectivity_value=count,ncount,mean_length,dti_fa --connectivity_type=pass,end --template=0

My question is do you have any recommendations on how I could alter the parameters that is more likely I would get fully connected networks? If not, is there a way to use DSI Studio to convert the .fib files into a file usable by MRtrix or FSL for probabilistic tracking?

Thank you so much for your time!

Best,

Lexi

[Frank Yeh]

I would first try dsi_studio --action=trk --source=*.fz
--connectivity=Brainnectome --tract_count=10000000 --output=no_file
and see whether it works.
Then you may troubleshoot by adding each parameter back to see which
one gets in the way.

Best,
Frank

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[Alexa Mousley]

Hi Frank,

Thanks for the advice! I tried those parameters on 200 networks and unfortunately 38 networks were still disconnected.

Best,

Lexi

[Frank Yeh]

I would look at the unconnected networks directly within the GUI and
observe if the tractography is able to reach those regions.
This approach could provide some valuable insights into the underlying
cause of the problem.
Frank

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[Frank Yeh]

BTW, I would avoid using 'end' which is much more restrictive and may
cause many unconnected nodes.
Frank