Onboarding

First of all, welcome!

We hope we may provide a nice new academic home for you at the netstim.

On this page, we want to give some useful quick tips regarding the “onboarding process” to quickly become productive at the netstim. More detailed information related to Brigham / Harvard onboarding can be found in the internal manual.

Checklist: Must do's

• Get a Slack account and get on the following three Slack channels:

  • The Netstim lab channel

  • The CBCT lab channel braincircuit.slack.com

  • The Lead-DBS user channel -> Autoinvite yourself here.

  • If you join the Lead-DBS development work, you should also get on the Lead-DBS dev channel

• Get an account to edit our online resources (-> talk to Leon or Qiang Wang).

  • The netstim website.

  • The Lead-DBS website. With that you'll automatically have an account for the Lead-DBS forum.

  • Our gitbooks (including this one).

• Get a github account and familiarise yourself with git (-> talk to Ningfei for questions).

• Get a twitter account (see below).

• Get some software installed (see below).

Useful resources

General resources

• Twitter. In my humble opinion, Science Twitter is the most important tool to conduct impactful research. In case you're on twitter, connect to us (see below). If you're new to it, maybe check out whom we follow to get some inspiration of what could be interesting, to you, too.

  • For some reasons why twitter may be helpful, see these blog posts by Caitlin Vander Weele or Micah Allen.

  • Twitter handles of people affiliated with the netstim: @leaddbs, @leadconnectome, @andreashorn_, @b_alfatly, @neumann_wj, @qiangwangdr, @c_neudorfer, @LLGoede, @NingfeiL, @b_hollunder, @simonoxen

• Researchgate. RG is yet another social media framework for academia but it helps to keep track of papers, get your research structured online and find helpful papers that are related to your work. Also, RG is Berlin based, so why not support the locals.

Computer resources: Mac

We can recommend working with a mac (or if not with linux) in neuroscience – it’s a joy to work with them. The reason is the unixoid foundation of the OS, i.e. the possibility to use a lot of command-line based software suites that are not available for windows (for instance major software pipelines like FSL and FreeSurfer are not but it doesn’t end there). Finally, logging into remote clusters via ssh is seamless on mac or linux – while a bit cumbersome on windows.

Basic software that you’ll probably need

• Matlab (-> Ask Jan for a license) - Make sure you have the Image Processing, Signal Processing, Statistics and Machine Learning Toolboxes, these are used by Lead-DBS.

• SPM12 installed on the Matlab path

• Lead-DBS, our in-house DBS imaging and connectivity suite with which we do almost everything

• 3DSlicer – a great nifti viewer and complete neuroimaging suite

• Chris Rorden’s beautiful SurfIce visualization tool

• FSLeyes [link]

In case you use a mac, here are some great tools that you may want to check out:

• The quicklook nifti viewer – must have, it will make your life much easier!

• SmartGit – a GUI for git we can recommend. But any Git GUI (or command line if you prefer so) is fine of course.

Office / Figure building

• Affinity Designer for figures

Other OS-independent software recommendations

• Franz Multimessenger – a great messenger app that will make it easier to connect you to Slack and other services

• MRIcron – a light-weight nifti viewer

• Mango – another light-weight nifti viewer (and yes, it’s good to have a few of those)

• ITKsnap – another nice nifti tool