Computing FA along the CST connecting between 2 ROIs

[Vikram]

Hi Frank,

Thanks so much for developing such wonderful software! So far, I have been able to do all the necessary preprocessing, and get to the point where I can do tractography analysis (Step T3). 

I want to reproduce the analysis pipeline used here - https:/doi.org/10.3389/fnins.2016.00079 where, the authors computed the Fractional Anisotropy in the CST between the Posterior Limb of the Internal Capsule (PLIC) and certain motor areas (M1, PMC, SMA). 

In DSI studio, after uploading the .fib file, in Step T3A, I have used the JHU atlas (https://neurovault.org/images/1401/) to load the right and left PLIC (region 20 & 21) as the "seed" region and used the Brodmann Atlas to load the M1 (BA4L, BA4R) as "end" region. I plan to compute the tract-specific FA values in the left and right CST. However, I am not sure about the next steps in Step T3c and T3d. Could you please help? 

Let's say I am able to do it manually for one subject, how do I automate the whole process for all the subjects using batch scripting? I want to know what additional parameters do I need to put in the command (as per the tutorial in http://dsi-studio.labsolver.org/Manual/command-line-for-dsi-studio)

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Vikram

[Frank Yeh]

Hi Vikram,

    A similar manual process can be reproduced using the command line, but writing the command line script can be a challenge.

    A quick solution is to use batch automatic fiber tracking to map CST for you: http://dsi-studio.labsolver.org/Manual/automatic-fiber-tracking

Best regards,

Frank

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