Ilumr Pulse Sequence plotting tool

General
1

Here is a beta version of a tool you can use to develop and test pulse sequences offline. It will allow you to plot the RF/gradient/acquisition gate waveforms that will be generated when executed on the ilumr system.

Download and unzip: sequence_plotting_tools_24_02_12.zip - Google Drive

The README.md file inside contains more information on setup and usage.

To install JupyterLab and the required python libraries, follow the instructions in the next post: Ilumr Pulse Sequence plotting tool - #3 by Cameron

3

Step by step instructions for installing the pulse sequence plotting environment using JupyterLab Desktop:

  1. Download and install jupyterlab desktop: GitHub - jupyterlab/jupyterlab-desktop: JupyterLab desktop application, based on Electron.

  2. Download and extract: sequence_plotting_tools_24_02_12.zip - Google Drive

  3. Open jupyterlab desktop

  4. Top right menu->Manage Python Environments

    step4
    step41024Ă—768 30.7 KB

  5. Settings->Install bundled (if not already) then tick “Use bundled Python…”

    step5
    step5800Ă—600 24.6 KB

  6. Close both jupyterlab windows and reopen jupyterlab desktop

  7. Top right menu->Manage Python Environments

  8. Create New

  9. Check “New Environment”

  10. Name: sequence_plotting

  11. Type: conda

  12. Uncheck “Include jupyterlab”

  13. Additional Python packages: “jupyterlab==3.6.8 panel==1.4.5 numpy==1.26.4 PyYAML==5.4.1 pyzmq==26.2.0 scipy==1.11.4 zerorpc-python==0.6.3 msgpack-python==1.1.0 msgpack-numpy==0.4.8 matplotlib==3.9.2”

  14. Create

    step14
    step14862Ă—664 28 KB

  15. When finished close “Manage Python Environments” window

  16. New session…

  17. Environment menu->conda: sequence_plotting

    step17
    step171024Ă—768 42.2 KB

  18. Navigate to sequence_plotting directory in file browser and open notebooks->plot_RARE_example.ipynb

    step18
    step181024Ă—768 38 KB

  19. Run->Run All Cells

    step19
    step191371Ă—856 70.5 KB

If all is successful, you should see the waveforms of the RARE sequence plotted as seen above. The bokeh warnings may be ignored.

4

hey Cameron!

This is a very nice tool. Is there an update to it to reflect the latest matipo release (2.2.0 https://www.resonint.com/post/ilumr-software-update)? Or perhaps that isn’t needed?

Cheers,
Aaron

5

The included matipo library in the sequence plotting tools zip file is not the latest matipo version, however it still works correctly for pulse sequence plotting as there haven’t been changes to the pulse sequence programming in the 2.2.0 update.

Are you experiencing any issues?

Cameron

6

Thanks for the clarification Cameron - I’ve not had any issues but we updated the software on our Ilumr yesterday so I wanted to check just in case.

Cheers,
Aaron

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