Skip to content

Minor doc improvements #263

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Minor doc improvements #263

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
599d0d0
add sentence about GPU node selection
KrisThielemans Jul 8, 2025
0e0218b
add line referring to Brainweb web-page
KrisThielemans Jul 8, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 4 additions & 1 deletion DocForParticipants.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,7 @@ installation of all dependencies and downloading the example data.
[![CPU Codespace](https://img.shields.io/badge/Codespaces-CPU-blue?logo=github)](https://codespaces.new/SyneRBI/SIRF-Exercises) [![GPU Codespace](https://img.shields.io/badge/Codespaces-GPU-green?logo=github)](https://codespaces.new/SyneRBI/SIRF-Exercises?devcontainer_path=.devcontainer%2Fgpu%2Fdevcontainer.json&geo=UsEast&machine=standardLinuxNcv3)

Some notes:
- Please select a GPU-node to run the GPU Codespace (you might have to try look in different "regions", and availability varies).
- You will have to select a Python kernel for each notebook (top-right). Please use the existing `conda` python kernel (**not** `/usr/bin/python3`) listed in "Python environments". Alternatively, you can access the jupyter server running in the codespace via [port forwarding](https://docs.github.com/en/codespaces/developing-in-a-codespace/forwarding-ports-in-your-codespace).
- You might want to conserve some resources by manually
[stopping a code space](https://docs.github.com/en/codespaces/developing-in-codespaces/stopping-and-starting-a-codespace),
Expand All @@ -96,6 +97,8 @@ Follow instructions given elsewhere.

### Using the VM

See our [VM instructions](https://github.com/SyneRBI/SIRF-SuperBuild/blob/master/VirtualBox/README.md) for information.

1. start the VM from VirtualBox (user `sirfuser`, password `virtual`)
2. Open terminal (either via `Activities` or pressing `ctrl-alt-T`) and type

Expand Down Expand Up @@ -163,7 +166,7 @@ cells for running the script, but you can also do this from the command line (se
cd /wherever/you/installed/it/SIRF-Exercises
scripts/download_data.sh -m -p
```
On the VM and Azure, the exercises are installed in `~/devel`, in docker in `/devel`, and in the STFC Cloud in `~`. (Apologies for that!).
On the VM and Azure, the exercises are installed in `~/devel`, in docker in `~/work/devel`, and in the STFC Cloud in `~`. (Apologies for that!).

This will be a ~3 GB download.

Expand Down
2 changes: 1 addition & 1 deletion notebooks/Introductory/introduction.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -220,7 +220,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"We will download and use Brainweb data, which is made more convenient by using the Python brainweb module. We will use a FDG image for PET. MR usually provides qualitative images with an image contrast proportional to difference in T1, T2 or T2* depending on the sequence parameters. Nevertheless, we will make our life easy, by directly using the T1 map provided by the brainweb for MR."
"We will use Brainweb data, which is a dataset containing MRI scans as well as anatomical models of the normal brain, see https://brainweb.bic.mni.mcgill.ca/brainweb/anatomic_normal.html. Using this data is made more convenient by using the Python brainweb module. We will use a FDG image for PET. MR usually provides qualitative images with an image contrast proportional to difference in T1, T2 or T2* depending on the sequence parameters. Nevertheless, we will make our life easy, by directly using the T1 map provided by the brainweb for MR."
]
},
{
Expand Down