--cmd is not used/recognized

[Josh Neudorf]

Hi Frank,

I am trying to use the --cmd flag on the --action=rec step and it gives the error: "--cmd is not used/recognized". Is the --cmd flag still available? We are trying to apply a b-table flip but are not able to without this --cmd flag as far as I am aware.

Thanks,

Josh Neudorf

[Josh Neudorf]

Hi Frank,

Following up to share the fix my student found:

The error appears only if a reconstructed .fz file is already present in the directory, hence why overwrite was necessary. Given that, still the error should explain necessity of overwrite flag and not about cmd. I'm explaining below:

• This code works for reconstruction and b-table correction
  • `dsi_studio --action=rec --source=*.sz --cmd="[Step T2][B-table][Check B-table]"`
• But if a corresponding reconstructed .fz is file is already presented, reconstruction gets interrupted without creating the .fz file with this error:
  • │ ├──overwrite=0 │ ├──output file exist at "/home/cumminelab/drive_4tb/PREDYS/data/derivatives/test_qsi-dsi/sub-01_space-ACPC_desc-preproc_dwi.gqi.fz" │ └──⏱1s327ms └──⏱1s327ms ❗--cmd is not used/recognized.
• But running this did not give any errors and successfully runs reconstruction with b-table correction and replaced the previous .fz file 
  • `dsi_studio --action=rec --source=*.sz --cmd="[Step T2][B-table][Check B-table]" --overwrite=1`

Best wishes,

Josh Neudorf

[Frank Yeh]

Hi Josh,

Thank you for tracking this down and sharing the details. You are right—the error message is misleading when the output file already exists and overwrite is disabled. I will revise it so that it reports the existing output file and the need for --overwrite=1, rather than saying that --cmd is not recognized.

Best,
Frank

On Fri, 17 Jul 2026 14:50:06 -0700 (PDT), Josh Neudorf jneu...@ualberta.ca wrote:

Hi Frank,

Following up to share the fix my student found:

The error appears only if a reconstructed .fz file is already present in the directory, hence why overwrite was necessary. Given that, still the error should explain necessity of overwrite flag and not about cmd. I’m explaining below:

• This code works for reconstruction and b-table correction

• dsi_studio --action=rec --source=*.sz --cmd="[Step T2][B-table][Check B-table]"

• But if a corresponding reconstructed .fz is file is already presented, reconstruction gets interrupted without creating the .fz file with this error:

• │ ├──overwrite=0 │ ├──output file exist at “/home/cumminelab/drive_4tb/PREDYS/data/derivatives/test_qsi-dsi/sub-01_space-ACPC_desc-preproc_dwi.gqi.fz” │ └──⏱1s327ms └──⏱1s327ms ❗–cmd is not used/recognized.

• But running this did not give any errors and successfully runs reconstruction with b-table correction and replaced the previous .fz file

• dsi_studio --action=rec --source=*.sz --cmd="[Step T2][B-table][Check B-table]" --overwrite=1

Best wishes,

Josh Neudorf

On Friday, July 17, 2026 at 7:22:07 AM UTC-6 Josh Neudorf wrote:

Hi Frank,

I am trying to use the --cmd flag on the --action=rec step and it gives the error: “–cmd is not used/recognized”. Is the --cmd flag still available? We are trying to apply a b-table flip but are not able to without this --cmd flag as far as I am aware.

Thanks,

Josh Neudorf

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[Josh Neudorf]

Wonderful - thank you Frank. 

Best, 

Josh

Josh Neudorf, PhD

Assistant Professor, Psychology, Athabasca University 

Adjunct Professor, Psychology, University of Alberta

Adjunct Professor, Communication Sciences and Disorders, University of Alberta

Faculty Member, Neuroscience and Mental Health Institute (NMHI), University of Alberta

Affiliate Member, Institute for Neuroscience and Neurotechnology (INN), Simon Fraser University

Consulting Editor, Cortex 

1-306-850-4761 

1-844-636-2395

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From: dsi-s...@googlegroups.com <dsi-s...@googlegroups.com> on behalf of Frank Yeh <fran...@gmail.com>
Sent: Saturday, 18 July 2026 11:19:46
To: dsi-s...@googlegroups.com <dsi-s...@googlegroups.com>
Subject: [dsi-studio] Re: --cmd is not used/recognized

 

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