Tract_id in CLI

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Allison Yan

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Nov 23, 2023, 1:36:04 PM11/23/23
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Hi Frank,

When I used the tract_id=Corticospinal_Tract_L, it could not find it and the report showed an error as below:Screen Shot 2023-11-23 at 1.27.33 PM.png.

I found the Corticospinal_Tract_L in Long_Projection_Pathways.tt.gz.txt, but I am wondering how I can tell dsi studio to use do the tracking with tract_id that didn't in Association_Pathways.tt.gz?

Best,
Allison

Frank Yeh

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Nov 23, 2023, 3:54:47 PM11/23/23
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You may update DSI Studio again and see if it works.
Frank

Allison Yan

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Nov 23, 2023, 5:10:52 PM11/23/23
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I have updated it and it still didn't work and the error is the same.

Frank Yeh

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Nov 23, 2023, 10:09:24 PM11/23/23
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The following command works on my version:

--action=trk --source=*.fib.gz --track_id=CorticospinalTractL --fiber_count=5000

Depending on the version, the track_id has to match the name shown in the GUI's autotrack.

Best regards,
Frank





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Allison Yan

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Nov 24, 2023, 6:35:20 PM11/24/23
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Hi Frank,

I am using the latest.sif to run all the commands. So it should be the latest version, right?

I tried your command but the error remained the same. I double-checked the GUI, mine is Corticospinal_Tract_L. But it still didn't work on my side.

The command I used is:
singularity exec /pathway/dsistudio_latest.sif dsi_studio --action=trk --source=*.fib.gz --track_id=Corticospinal_Tract_L --seed_count=1000000 --fa_threshold=0 --min_length=30 --max_length=200 --turning_angle=0 --step_size=0 --tolerance=24 --output=*.CSTR.tt.gz --export=stat

Do you have any idea why it cannot extract the Corticospinal tract? I tried it with Frontal Aslant tract and it worked well.

Best,
Allison

Frank Yeh

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Nov 24, 2023, 9:43:15 PM11/24/23
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--track_id=CorticospinalTractL

Allison Yan

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Nov 25, 2023, 4:27:32 PM11/25/23
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I tried it but it didn't work:
Screen Shot 2023-11-25 at 4.26.25 PM.png.

Frank Yeh

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Nov 25, 2023, 9:12:52 PM11/25/23
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Sorry, you are still using the older versions.

You may  need to recreate the sif to get the most updated version of DSI Studio.

Best regards,
Frank

Allison Yan

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Nov 27, 2023, 2:52:42 PM11/27/23
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Hi Frank,

I updated it and it worked! Thank you!

Frank Yeh

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Nov 27, 2023, 4:00:49 PM11/27/23
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Glad it worked!
If there is any remaining issue, please feel free to let me know.
Frank

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