Command-line visualization export capabilities for reproducible figures in --action=vis

[ali kazemi]

Hi Frank and DSI Studio Community,

I am currently trying to build a fully reproducible, scripted pipeline to generate publication figures using DSI Studio, and I’m hitting a wall regarding the command-line interface for visualization.

Context & Environment:

• DSI Studio Build: Ubuntu 24.04 build, "Hou" version, Jun 15 2026 (doi:10.1038/s41592-025-02762-8)

• Environment: Running inside WSL2 with WSLg handling X11/Wayland display and Mesa software OpenGL.

• Status: Confirmed that running dsi_studio --action=vis successfully launches the GUI window and renders correctly in this setup.

Goal:

I want to generate a publication figure showing several AAL-atlas cortical regions (e.g., pars triangularis, pars opercularis, insula, Heschl's gyrus) color-overlaid on a T1/T2 template, fully from the command line without manual GUI interaction, so it can be automated within a script.

What I've Tried:

I attempted to pass screenshot/save tokens to the --cmd flag, but each returned an unknown command error:

Bash

dsi_studio --action=vis --source=<template.nii.gz> --cmd="screenshot" dsi_studio --action=vis --source=<template.nii.gz> --cmd="save_image:/path/out.jpg" dsi_studio --action=vis --source=<template.nii.gz> --cmd="save_image,/path/out.jpg"

Each of these returns unknown command: <name>, printed once per token. The CLI --help and documentation pages don't seem to enumerate the valid arguments or syntax accepted by --cmd under --action=vis.

Questions:

1. Is there a currently supported way to drive --action=vis scriptably to export a static screenshot/image of a loaded template with atlas-region overlays (the CLI equivalent of File → Save Screenshot)? If so, what is the correct syntax/token?

2. Is there a canonical list or documentation page of all valid --cmd values for the visualization action?

3. If this headless/scripted rendering path doesn't exist today, is atlas-overlay image export on the CLI roadmap, or is rendering anatomical figures intended to remain strictly GUI-only?

Current Workaround & Motivation:

As a temporary fix, I reconstructed the figure manually in Python using nibabel and matplotlib by directly loading the template and the files under atlas/human-neonate/. While this works, it duplicates rendering logic that DSI Studio already handles beautifully in the GUI, and it lacks the robustness of staying natively in sync with DSI Studio’s internal region boundaries and future atlas updates.

Any guidance, syntax corrections, or insights on the CLI roadmap for this feature would be greatly appreciated!

Best regards,

Ali Kazemi

[Frank Yeh]

You may check out the first week first at practicum.labsolver.org
about command history.
The command history can be invoked by the command line to accomplish GUI work.
There was a discussion in the forum in the past about this.
Frabj

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