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Tool

Here are the basic tools that you need to do research.

For windows users, you should consider to install the WSL.

1 python

We switched from matlab to python, because of the birth of deep learning and the death of matlab. You are expected to code in python, so you can use our toolbox. You can use any version >3.13 (a major improvement with parallel computing) and you can get the latest one from https://www.python.org/. virtualenv and Anaconda are not very necessary, because we usually maintain the code ourselves and stay with a single version. Some basic command and library that you should know: pandas, numpy, pip3

  • check python site-package path
python3 -m site
  • add my library by creating a my_path.pth file in my toolbox with
/Users/xxx/project/toolbox/mri_recon/
  • create symbolic link in the site-path path
ln -s /Users/xxx/project/toolbox/mypath.pth mypath.pth

2 git

Our code is controlled using git and we also strongly suggest you control your code using git too. More details.

3 remote

We work on several servers and you should use ssh. You should know ssh, scp, .ssh/config, public key and so on. More details. Usually we don't work on User interface on server, but if it is necessary, such as sequence development, you can use Microsoft Remote Desktop.

4 IDE

vscode is recommended. In case you have any questions, the lab has more experiences on it. A few extension of vscode is recommended, including git graph, python, remote package, sftp.

Coding agents are becoming more popular, you can use codex, claude, opencode, pi-coding agent.

If you are interested, I would also recommend the vim or neovim, an old but more efficient IDE working with agents. A high learning curve should be warned ahead.

5 viewer

You need ITKSnap to view Nifti file and manual segmentation. You need horos to view dicom.

6 reference manager

Zoteros zoteros.

7 notes

We highly recommend that you keep your notes in markdown format. You can use obsidian or typora. You can also use it in onenote.

8 writing

Your zju account can have a free office365 online account, which has a huge onedrive and can use word online (can be downloaded and open in your desktop office too). If you have multiple computer, it is also good to use onedrive to sync files. When we write paper together, please share it through office365, so we can work on it together.

We also switch the paper draft to markdown, and especially critic markdown. Everything will be in flat text.

9 meeting

tencent meeting is a commonly used one. But we may also need dingding and zoom.