Command line for max seed and max track

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Isabella Stallworthy

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Jun 25, 2025, 9:34:21 AM6/25/25
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Hello! 

For fiber tracking with the new DSI Studio, I am wondering if there are command lines to set max seeds and max tracts? 

Thanks,
Isa

Frank Yeh

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Jun 25, 2025, 9:41:06 AM6/25/25
to ist...@seas.upenn.edu, DSI Studio
Yes, --tract_count sets the max tracts and --seed_count sets the max seed count.
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Isabella Stallworthy

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Jun 25, 2025, 10:19:59 AM6/25/25
to Frank Yeh, DSI Studio
Thank you. It is working for --seed_count but for --tract_count I get the following error:

❗--tract_count is not used/recognized. Did you mean --thread_count ?

Isabella (Isa) Stallworthy, PhD  
JSMF Postdoctoral Fellow 
Complex Systems Lab
University of Pennsylvania
ist...@seas.upenn.edu
she/her/hers
Twitter: @isaStallworthy
Isabellastallworthy.com




On Jun 25, 2025, at 9:40 AM, Frank Yeh <fran...@gmail.com> wrote:

Yes, --tract_count sets the max tracts and --seed_count sets the max seed count.

On Wed, Jun 25, 2025 at 9:34 AM Isabella Stallworthy
<ist...@seas.upenn.edu> wrote:

Hello!

For fiber tracking with the new DSI Studio, I am wondering if there are command lines to set max seeds and max tracts?

Thanks,
Isa

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Frank Yeh

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Jun 25, 2025, 10:23:32 AM6/25/25
to Isabella Stallworthy, DSI Studio
It is unlikely an older version of DSI Studio, or the command line ends
early due to existing target files.
Best,
Frank

On Wed, Jun 25, 2025 at 10:19 AM Isabella Stallworthy

Isabella Stallworthy

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Jun 25, 2025, 4:50:46 PM6/25/25
to DSI Studio
Thank you! I appreciate it. --seed_count seems to work but I get the following error for --tract_count:

❗--tract_count is not used/recognized. Did you mean --thread_count ?

thanks,
Isa

Isabella Stallworthy

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Jun 25, 2025, 4:50:50 PM6/25/25
to DSI Studio
Thank you! --seed_count worked but I am getting this error for tract_counts:

❗--tract_count is not used/recognized. Did you mean --thread_count ?


On Wednesday, June 25, 2025 at 9:41:06 AM UTC-4 Frank Yeh wrote:

Isabella Stallworthy

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Jun 25, 2025, 4:50:53 PM6/25/25
to DSI Studio
Thank you. It is working for --seed_count but for --tract_count I get the following error:

❗--tract_count is not used/recognized. Did you mean --thread_count ?


On Wednesday, June 25, 2025 at 9:41:06 AM UTC-4 Frank Yeh wrote:

Frank Yeh

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Jun 25, 2025, 4:52:50 PM6/25/25
to ist...@seas.upenn.edu, DSI Studio
You may try --fiber_count (older versions). New versions use --tract_count
> To view this discussion visit https://groups.google.com/d/msgid/dsi-studio/a4a093c7-937f-4b8c-be64-c7139a0b26e4n%40googlegroups.com.

Isabella Stallworthy

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Jun 25, 2025, 6:34:17 PM6/25/25
to Frank Yeh, DSI Studio
Thank you! My last questions are, for generating a connectivity matrix using the command line, using the older versions of DSI Studio,

1)  how to change “pass in region” to “end in region”
2) and how to change the output from count to count or dti_fa?

Thanks so much!


Isabella (Isa) Stallworthy, PhD  
JSMF Postdoctoral Fellow 
Complex Systems Lab
University of Pennsylvania
ist...@seas.upenn.edu
she/her/hers
Twitter: @isaStallworthy
Isabellastallworthy.com



On Jun 25, 2025, at 4:52 PM, Frank Yeh <fran...@gmail.com> wrote:

You may try --fiber_count (older versions). New versions use --tract_count

On Wed, Jun 25, 2025 at 4:50 PM Isabella Stallworthy
<ist...@seas.upenn.edu> wrote:

Thank you. It is working for --seed_count but for --tract_count I get the following error:

❗--tract_count is not used/recognized. Did you mean --thread_count ?


On Wednesday, June 25, 2025 at 9:41:06 AM UTC-4 Frank Yeh wrote:

Yes, --tract_count sets the max tracts and --seed_count sets the max seed count.

On Wed, Jun 25, 2025 at 9:34 AM Isabella Stallworthy
<ist...@seas.upenn.edu> wrote:

Hello!

For fiber tracking with the new DSI Studio, I am wondering if there are command lines to set max seeds and max tracts?

Thanks,
Isa

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You received this message because you are subscribed to the Google Groups "DSI Studio" group.
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Frank Yeh

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Jun 26, 2025, 12:34:24 AM6/26/25
to Isabella Stallworthy, DSI Studio
> 1) how to change “pass in region” to “end in region”

--connectivity_type=end

> 2) and how to change the output from count to count or dti_fa?

--connectivity_value=dti_fa

I would recommend not to use whole-brain tractography for computing
the 'connectivity' due to low reliability and lack of biophysical
meaning
The tract-to-region connectome would be a more reliable measurement.

Best regards,
Frank

Isabella Stallworthy

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Jun 26, 2025, 7:56:11 AM6/26/25
to Frank Yeh, DSI Studio
Thank you! 

And I totally agree with your point about tract-to-region connectome. We are currently working on adapting some of our analytic pipelines to be able to work with the tract-level information instead. 

Isabella (Isa) Stallworthy, PhD  
JSMF Postdoctoral Fellow 
Complex Systems Lab
University of Pennsylvania
ist...@seas.upenn.edu
she/her/hers
Twitter: @isaStallworthy
Isabellastallworthy.com



Frank Yeh

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Jun 26, 2025, 8:24:30 AM6/26/25
to Isabella Stallworthy, DSI Studio
Sounds great! Wish all the best with your study.
Best,
Frank
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