Netstim Lab Manual
  • Welcome to the Netstim Laboratory
  • Netstim Code of Conduct
  • Onboarding
  • Conferences / Travels
  • Publications
  • Affiliations
  • BIH Cluster
    • Access
    • Setup
  • Cloud Resources
    • Onedrive
    • Teams
    • Slack
    • Pcloud
  • Collection of Resources
  • Nomenclature
  • Internal Manual
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On this page
  • First of all, welcome!
  • Checklist: Must do's
  • Useful resources
  • General resources
  • Computer resources: Mac

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Onboarding

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Last updated 11 months ago

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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 CBCT lab channel braincircuit.slack.com

    • -> .

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

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

    • The .

    • The . With that you'll automatically have an account .

    • Our gitbooks (including this one).

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

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.

  • FSLeyes [link]

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

Office / Figure building

Other OS-independent software recommendations

. 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 or .

. 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.

installed on the Matlab path

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

– a great nifti viewer and complete neuroimaging suite

Chris Rorden’s beautiful visualization tool

The – must have, it will make your life much easier!

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

for figures

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

– a light-weight nifti viewer

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

– another nice nifti tool

The Netstim lab channel
The Lead-DBS user channel
Autoinvite yourself here
Lead-DBS dev channel
netstim website
Lead-DBS website
for the Lead-DBS forum
github account
Twitter
these blog posts by Caitlin Vander Weele
Micah Allen
Researchgate
SPM12
Lead-DBS
3DSlicer
SurfIce
quicklook nifti viewer
SmartGit
Affinity Designer
Franz Multimessenger
MRIcron
Mango
ITKsnap