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Tool

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

For windows users, you may 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 >3.8 and you can get the latest one from https://www.python.org/. virtualenv and Anaconda are not necessary, because we usually 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 controled using git and we also strongly suggest you control your code using git too. You should contact Admin to have an account on Hal9000 first. 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 neccessary, 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.

5 viewer

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

6 reference manager

Before we used the sciwheel, now we are swithcing to 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 office365

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.

9 meeting

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