Hi @anibalsolon,

This project looks neat. Through the weird ways of the web, I somehow stumbled across it, and thought it might be nice to see how much effort it would be to try adding NiiVue (https://github.com/niivue/niivue) as the renderer. No worries if not, just thought it could be a nice pairing!

Right now, the image values are just scaled to 0-255.

Transforming the data into non-uniform bins would allow to threshold it and show the approximate value of a voxel (?).

I tried using vscode-neuro-viewer with visual-studio-code-bin 1.64.2-1 on Arch Linux.

This is the output after opening a file:

The same thing has happened for all NIfTI files that I've tested.

I can provide an example NIfTI file that failed for me (it is derived from publicly available data from the QSM Challenge 2.0):

https://ufile.io/9t6rlyri

The histogram flow is not super right now, there are some TODOs in the code.
Also, the mouse positioning related to the element and its conversion to a percentage could be abstracted as it is used in other views (e.g. slices slider).

NRRD files are very simple and similar to NIFTI files. It would be amazing if you could add support for them.

Hello 👋 I'm from the VS Code team.

Recently, we have been exploring a security feature we refer to as Workspace Trust. This feature is intended to centralize and unify a security conscious decision required by a variety of VS Code features. With workspace trust, the user will be able to declare whether or not they trust the folder that is opened in VS Code before these features are executed.

Why you should care

We want to make sure that those users have a delightful experience with workspace trust and that includes extension authors deciding how much of their extension is supported in an untrusted workspace. Custom editors are special in that if they cannot at least render in an untrusted state then they will be replaced by a lightweight message telling the user to enable trust. This means that users of your extension will not be able to see their editors and there may even be cases of data loss.

Workspace Trust experience

You can enable the feature with the following setting security.workspace.trust.enabled. Once enabled, you will see the following dialog when opening folders in VS Code.

This dialog is important for allowing the user to make a decision early and understand the impact of their decision. Once you understand the feature, you may want to customize when to display the dialog using the setting security.workspace.trust.startupPrompt.

You can follow the development of Workspace Trust and provide feedback in issue #106488.

Workspace trust API

First off, all of what I am about to say can be found in issue #120251. That issue will include discussion of the feature and any updates to the feature.

The Workspace Trust extension API is now in stable. This allowed us to release the first cut of our guide for onboarding your extension to Workspace Trust. The API is small, so here is a quick look.

You can declare your extension to provide complete, partial or no support in untrusted workspaces using the untrustedWorkspaces capability in package.json.

The following example declares that the extension is supported completely in untrusted workspaces. In this case, the extension is enabled in untrusted workspaces.

"capabilities": {
  "untrustedWorkspaces": {
    "supported": true
  }
}

The next example declares that the extension is not supported in untrusted workspaces. In this case, the extension is disabled in untrusted workspaces.

"capabilities": {
  "untrustedWorkspaces": {
    "supported": false
  }
}

The third option is to declared limited support. There are three tools provided to you when you select the limited option.

First, if you have a setting that can be configured in the workspace but requires the workspace to be trusted in order to apply the workspace value, then you can include the setting using restrictedConfigurations array property in untrustedWorkspaces object. Doing so, VS Code will ignore the workspace value of these restricted settings when your extension reads these settings values using the VS Code Workspace Configuration API.

The following example declares the settings that are restricted in untrusted workspaces.

"capabilities": {
  "untrustedWorkspaces": {
    "supported": "limited",
    "restrictedConfigurations": [
      "markdown.styles"
    ]
  }
}

Next, you can also check and listen if the current workspace is trusted or not programmatically using the following API:

export namespace workspace {
  /**
   * When true, the user has explicitly trusted the contents of the workspace.
   */
  export const isTrusted: boolean;
  /**
   * Event that fires when the current workspace has been trusted.
   */
  export const onDidGrantWorkspaceTrust: Event<void>;
}

Lastly, you can hide commands or views declaratively with the isWorkspaceTrusted context key in your when clauses.

A far more detailed guide on how to onboard which will be updated as we receive feedback can be found in issue #120251.

Rollout plan

We are planning on enabling this by default in the near future (most likely next release). To prepare for that day, we want to work with you to allow your editor to work seamlessly alongside the trusted workspace experience

Our Asks

The main features that should work for custom editors in an untrusted folder is rendering, viewing, and saving (if applicable). After reviewing your codebase, I believe that your extension doesn't execute user files as code and therefore is safe to use in an untrusted workspace. My suggestion would be to adopt supported: true

Please let me know if you have any question or would like to meet up via voice chat as I would be happy to assist you in getting your extension ready for workspace trust!

Things are too cramped on index.js.

For all my scans the images are displayed with the bbr color palette instead of the usual bw.

The color palette is chosen based on the min value of the nifti file.
https://github.com/anibalsolon/vscode-neuro-viewer/blob/main/webview/nifti/index.ts#L24-L26

I would either like to see the standard bw scale being used or a button to switch the color palette.

Consider the height of the slider to compute the relative positioning when clicking the slider. The center of the slider must be in the mouse position.

Hey Anibal!

Great extension! I was happily surprised to see you were the author. I was feeling lazy and needed to look at a bunch of nifti files on a server so I used the sshfs extension with your extension and it worked like a charm. So this issue is more a request than a bug report.

For open and libre reasons, I use VSCodium instead of VSCode, so I was wondering if you'd be willing to go for the extra mile and publish it to Open VSX in addition to the VS Code Marketplace? Open VSX is an open-source registry for VS Code extensions. It can be used by any development environment that supports such extensions.

I could install the extension by downloading the VSIX file, but it would be neat if NeuroViewer was directly on Open VSX! :) I have never published an extension myself, but I think it doesn't require much more from your side. Here's a link to the wiki explaining the publishing process.

Happy to help you in that regard if you need anything.

Thanks again for your great extension 🚀

• #7
• Compute coverage for unit tests
• Upload to Coveralls or other platform
• Bump version
• Automatic publish to vsce and ovsx
• Find different Niftis to add to test, with different headers and data

All the items above are related to finishing up Github Actions setup.

References:
https://github.com/microsoft/vscode-jupyter

• Global settings regarding default palettes and axis.
• Settings per workspace, if a workspace is being used
• Settings per session/window
• Settings per file? Maybe save it in the Nifti, or check if there's another API for VSCode

Add group toggle for X, Y, and Z.

https://code.visualstudio.com/api/extension-guides/web-extensions

Load the image to memory, access the Nifti parser from within the webview page.

• Detect errors in image parsing and store tracebacks
• Point user to open issue when an error is detected (Github extension integration?)
• File upload option (if smaller than 25MB- Github limit), WeTransfer?

Add simple 4D movie player.

Single-slice 3D niftis should be shown as 3D images with one dimension not scrollable. Instead they are reduced to 2D niftis. This results in two scroll-bars X,Y where the user scrolls through 1D visual arrays.

Hi @anibalsolon, great plugin. I've used it and it works seamlessly in VSCode. I have a separate use-case to propose and see if it's in the scope of your work.

Our group uses code-server on an HPC cluster which runs a VSCode backend in a singularity image, and forwards the port to a local machine. You can see how that's done here in docker and here in singularity. Our use case is here.

Our current only limitation is that we cannot open images that are on the cluster with NeuroViewer. When we select an image, it hangs on the Loading screen.

Let me know if this is something you'd consider adding as a feature, or if there is anywhere you can point me to start digging around as to how you load images -- maybe I can PR.

Thanks!

https://code.visualstudio.com/docs/getstarted/telemetry#_for-extension-authors

Report errors, image sizes, value types and ranges, picked color palletes

Auto screenshot?

I thought it was lacking DICOM series support, so added naive one https://github.com/kubzoey95/vscode-neuro-viewer/tree/dcm_support
Please tell me if you'd like it included into extension or if you see any issues.

Error message when trying to load an image:

Unable to open '...nii.gz'
Cannot read properties of undefined (reading 'map')

This file opens fine with ITK-SNAP. It was created by applying a mask (with c3d) to another image which opens fine with this tool.