A script for fiber tracking with a particular atlas

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Raul Gonzalez

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Sep 16, 2022, 8:39:44 PMSep 16
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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

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Sep 16, 2022, 8:43:23 PMSep 16
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which atlas would you like to use?
Frank

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Raul Gonzalez

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Sep 16, 2022, 8:48:42 PMSep 16
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Thanks for your answer. I have the JHU-ICBM atlas in a *.nii.gz

Fang-Cheng Yeh

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Sep 16, 2022, 9:08:06 PMSep 16
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It won't work because JHU atlas is not a streamline-based atlas.

Raul Gonzalez

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Sep 16, 2022, 9:25:32 PMSep 16
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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

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Sep 16, 2022, 9:32:27 PMSep 16
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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

Raúl González Gómez

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Sep 16, 2022, 9:48:35 PMSep 16
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Thank for your time Frank
best regards 
Ra

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