If you do not already have them, please obtain accounts at:
GitHub and ORCID are mandatory to use MorphoCloud. MorphoSource account is required, if you want to be able to download data (you can search for data without an account).
Also you will need a 3-button mouse (cannot emphasize this enough) to operate 3D Slicer (or any other 3D software) effectively. Optionally, install a preview version of Slicer with a revision number 34021 or higher (version we are using on MorphoCloud) on your own computer as a backup, in case you have issues with cloud connections.
Finally, having a second monitor is highly advised, since that will allow you to keep your zoom and cloud sessions on separate screens.
We will run this course through our cloud platform, MorphoCloud (MC) On Demand. Please read more about MorphoCloud instances at https://github.com/SlicerMorph/Tutorials/blob/main/MorphoCloud/README.md. For ideal performance, we suggest using a wired ethernet connection at your university's campus. A dedicated wifi network (like your home) should also work fine. Try to avoid public wifi access points due to unpredictable network performance.
Your MC instances are configured to be available 7/24 throughout the course. They will be taken offline on Friday night and be deleted. So if you have anything important make sure you download them at the end of the course. After the course, if you are interested in continuing to use the MorphoCloud Instances, you can follow the instructions at https://morphocloud.org
- Always keep your data in the MyData storage volume. This is your persistent storage, data stored elsewhere may get deleted.
- While using the Guacamole (the web browser connection) Use the
CTRL(CMD in Mac) + ALT + SHIFTcombination to make the cloud connection side window visible (or to make it disappear, if visible). This is where you can transfer file to and from cloud. - Apart from transfering files, we highly encourage you to install and use the TurboVNC software to connect to MC. Read more about your connection options at: https://github.com/SlicerMorph/Tutorials/blob/main/MorphoCloud/README.md#you-have-two-options-to-connect-to-gui
- For best user experience, switch to full screen mode in your browser window (not advisable if you do not have a second monitor, as you won't be able to see the zoom window).
- A: Side toolbar that gets activated by pressing the
CTRL (or CMD)+ALT+SHIFTkeys. It allows copy/paste into the remote session, browse and download files on the remote drive (only available if you are using web browser to connect to MC). - B: Shortcuts to commonly used applications and to MyData storage volume.
- C: Displays list of available applications (searchable)
- D: Right mouse clicking anywhere on desktop brings this menu, including changing screen resolution (Display settings).
- E: Click on this icon anytime to extend your session for additional 4 hours (not necessary for the course).
To be able to access the drive with the preloaded workshop data, you need to execute this command in a terminal window:
curl https://jetstream2.exosphere.app/exosphere/assets/scripts/mount_ceph.py | sudo python3 - mount \
--access-rule-name="MorphoCloudCephShare-ro" \
--access-rule-key="AQAIDi1nKwbRFRAA9KKHUddANj6Ywj8ag7N9pg==" \
--share-path="149.165.158.38:6789,149.165.158.22:6789,149.165.158.54:6789,149.165.158.70:6789,149.165.158.86:6789:/volumes/_nogroup/60bf684c-51d1-4abb-93f5-188d4d164111/1fe273cd-1e4d-4087-ad2b-01d548a16fe0" \
--share-name="MorphoCloudCephShare"
This is a one-time setup, unless the instance has to be deleted and re-created. Share will be mapped to:
/media/share/MorphoCloudCephShare
and it will be read-only. You should continue saving your data into the your MyData folder (located in /media/volume/MyData)
Uploading to remote: If your files are small (<100MB) and you have a stable connection, just dragging and dropping individual files to the browser window. Those files will be saved under your MyData volume, which is located at /media/volumes/MyData/. If your data is already on the cloud (e.g., MorphoSource, dropbox, google drive, etc), the fastest way is to use the Firefox browser built into the instance and directly download them to your remote session. Just remember to copy them to your MyData.
Downloading from the remote: If the file is small, you can use the interface shown above in the screenshot (Box D:), which works one file at a time.
If you have many files, or your files are large, we advise to use SFTP (Secure FTP) tools for bulk upload/download. There are many free tools, search one for your computer. Remember, any data you have generated and important for you, you should download to your own computer.