A script for fiber tracking with a particular atlas

[Raul Gonzalez]

Frank, thanks for this amazing toolbox. I want to run a fiber tracking, similar to the following script but with another atlas. How can I specify the other atlas?

Best regards

Raul

path=C:\Users\Alumnos\Ra\Programs\neurotools\dsi_studio_64
for /f "delims=" %%x in ('dir *.fib.gz /b /d /s') do (
call dsi_studio.exe --action=atk --source="%%x" --export=stat,tdi > "%%x.log.txt")

[Fang-Cheng Yeh]

which atlas would you like to use?

Frank

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[Raul Gonzalez]

Thanks for your answer. I have the JHU-ICBM atlas in a *.nii.gz

[Fang-Cheng Yeh]

It won't work because JHU atlas is not a streamline-based atlas.

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[Raul Gonzalez]

I do not understand. The problem is that JHU is not in the MNI space, or is not included in the original atlas of DSI studio. I can already aggregate new atlases into the DSI studio (not included in the toolbox previously). Can you recommend some lines of action for me?

[Fang-Cheng Yeh]

The automatic tracking in DSI Studio use "trajectory-based recognition", not "voxel-based recognition."

The last two paragraphs of the Discussion at https://www.nature.com/articles/s41467-022-32595-4 explains the details. Some discussions are provided in the responses to the review comments.

Frank

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[Raúl González Gómez]

Thank for your time Frank

best regards 

Ra

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