Batching

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Arian Klows

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Apr 26, 2022, 10:59:58 AMApr 26
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Hello Frank,

I was trying to explore the network measures in dsi studio. 

I figured out how to derive the network measures such as clustering coefficient, local efficiency etc for each subject. But don’t know how to do it for multiple subjects. 

Is there a way to extract the network measures using a batch function? Please help. Thanks. 

Frank Yeh

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Apr 26, 2022, 11:10:05 AMApr 26
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Arian Klows

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Apr 26, 2022, 11:19:17 AMApr 26
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Arian Klows

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Apr 26, 2022, 12:03:31 PMApr 26
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Hi Frank,

For deriving network measures from multiple subjects, I created a folder with all FIB files. Inside the folder, I created another .bat file with the following:
path=C:/Users/ARIAN/Desktop/dsi_studio
for /f "delims=" %%x in ('dir *.fib.gz /b /d /s') do (
    call dsi_studio.exe --action=trk --source="%%x" --seed_count=1000000 --thread_count=8 --output=no_file --connectivity=AAL > "%%x.log.txt"
)

Then I pressed run command line and selected the folder with FIB files and .bat, but nothing happened. Am I doing something wrong?

Frank Yeh

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Apr 26, 2022, 12:07:22 PMApr 26
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If this is your first time using the DSI Studio command line, I would suggest trying other simpler commands first just to make sure it works.
Best regards,
Frank


Arian Klows

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Apr 26, 2022, 12:12:43 PMApr 26
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I just simply typed 

path=C:/Users/ARIAN/Desktop/dsi_studio

But it’s throwin an error 
Cannot parse:path

Why is it so? Any suggestions?

Frank Yeh

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Apr 26, 2022, 12:31:29 PMApr 26
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Sorry, this is beyond the scope of DSI Studio.
You can check out videos teaching how to use Windows batch. (e.g.
search windows batch on Youtube).

Frank
> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAE5BcJnPkBKRNVsmnuWag2n%2BfmQbtf6cvnAXeE%3DZ447Fwh_LwQ%40mail.gmail.com.

Arian Klows

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Apr 26, 2022, 12:56:47 PMApr 26
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I figured it out. Thanks.

The script is working. But there is an error. I don’t have aal atlas in my dsi studio folder. 

searching AAL from the atlas pool...
ERROR: did not find atlas at C:/Users/ARIAN/Desktop/dsi_studio/atlas/AAL.nii.gz
ERROR: file or atlas does not exist:AAL

The folder which has atlas looks like the attached image.



ICBM152 folder has AAl atlas though. Should I copy past it outside this folder and rename it? 



Frank Yeh

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Apr 26, 2022, 1:12:28 PMApr 26
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You may check the Atlas button at Step T3a to see what atlases are available.
Frank

Arian Klows

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Apr 26, 2022, 1:22:53 PMApr 26
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Thanks Frank and sorry to bother you with my problems. 

I put the atlas to the path and it started running. But the output is so strange with 0s and nans :(

Any idea why is it so? 

Frank Yeh

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Apr 26, 2022, 1:41:36 PMApr 26
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Could you post the full command you use and the log output?

Arian Klows

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Apr 26, 2022, 3:20:16 PMApr 26
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The full command was

path=C:/Users/ARIAN/Desktop/dsi_studio
for /f "delims=" %%x in ('dir *.fib.gz /b /d /s') do (
    call dsi_studio.exe --action=trk --source="%%x" --seed_count=1000000 --thread_count=8 --output=no_file --connectivity=AAL2 > "%%x.log.txt"
)
  Attaching the output. Thank you. 
3104.src.gz.icbm152.qsdr.1.25.R71.fib.gz.log.txt
3104.src.gz.icbm152.qsdr.1.25.R71.fib.gz.tt.gz.AAL2.count.end.connectogram.txt
3104.src.gz.icbm152.qsdr.1.25.R71.fib.gz.tt.gz.AAL2.count.end.network_measures.txt

Frank Yeh

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Apr 26, 2022, 3:29:10 PMApr 26
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The data seems to have quality issues. Please check DWI and
tractography quality: https://www.youtube.com/watch?v=stL4GMeTC1I
You will also need to verify the accuracy using GUI before going for
the command line.
Hop this helps,
Frank

Arian Klows

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Apr 27, 2022, 12:48:16 PMApr 27
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Thank you very much for letting me know. 
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