User Tools

Site Tools


analysis:nsb2015:week1

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
Next revision Both sides next revision
analysis:nsb2015:week1 [2015/07/19 21:58]
mvdm [A first commit and push]
analysis:nsb2015:week1 [2016/01/04 17:51]
course-w16
Line 14: Line 14:
   * Optional: [[http://​www.youtube.com/​GitHubGuides|Introduction to version control with GitHub]] ([[http://​git-scm.com/​book/​en/​Getting-Started-Git-Basics|more detailed doc pages]], [[http://​stackoverflow.com/​questions/​tagged/​git|git tagged questions on StackOverflow]],​ [[https://​github.s3.amazonaws.com/​media/​progit.en.pdf|Pro Git manual]], surprisingly readable)   * Optional: [[http://​www.youtube.com/​GitHubGuides|Introduction to version control with GitHub]] ([[http://​git-scm.com/​book/​en/​Getting-Started-Git-Basics|more detailed doc pages]], [[http://​stackoverflow.com/​questions/​tagged/​git|git tagged questions on StackOverflow]],​ [[https://​github.s3.amazonaws.com/​media/​progit.en.pdf|Pro Git manual]], surprisingly readable)
   * Optional: MATLAB documentation on [[http://​www.mathworks.com/​help/​matlab/​matlab_env/​understanding-file-locations-in-matlab.html|File Locations]] and [[http://​www.mathworks.com/​help/​matlab/​matlab_env/​what-is-the-matlab-search-path.html#​br8ch8o|Search Paths]]   * Optional: MATLAB documentation on [[http://​www.mathworks.com/​help/​matlab/​matlab_env/​understanding-file-locations-in-matlab.html|File Locations]] and [[http://​www.mathworks.com/​help/​matlab/​matlab_env/​what-is-the-matlab-search-path.html#​br8ch8o|Search Paths]]
 +
 +**NOTE**: if you are using NS&B lab computers, some or all of the steps below may already have been done. I recommend you read through them anyway, but check if things are already installed or set up before duplicating things!
  
 Step-by-step:​ Step-by-step:​
Line 36: Line 38:
 If you don't already have a %%GitHub%% account, go to [[http://​www.github.com|GitHub]] and sign up. E-mail me (mvdm at dartmouth dot edu) your account name, so I can give you access to the code repository. If you don't already have a %%GitHub%% account, go to [[http://​www.github.com|GitHub]] and sign up. E-mail me (mvdm at dartmouth dot edu) your account name, so I can give you access to the code repository.
  
-Meanwhile, download and install the Git client of your choice if you don't already have one installed. For Windows, I recommend [[http://​windows.github.com/​|GitHub Windows]] as a user-friendly way to get started. For installing Git and setting up GitHub on various operating systems, see [[https://​help.github.com/​articles/​set-up-git|GitHub:​ Set Up Git]]; note that on the NS&B computers, you need to select "Run as administrator"​ when running the installer.+Meanwhile, download and install the Git client of your choice if you don't already have one installed. ​(On NS&B lab computers, it is probably already installed; in that case you can open it and sign in with your account.) ​For Windows, I recommend [[http://​windows.github.com/​|GitHub Windows]] as a user-friendly way to get started. For installing Git and setting up GitHub on various operating systems, see [[https://​help.github.com/​articles/​set-up-git|GitHub:​ Set Up Git]]; note that on the NS&B computers, you need to select "Run as administrator"​ when running the installer.
  
 Next, configure your client. For %%GitHub%% Windows, after starting up the %%GitHub%% %%GUI%% (the default window that opens when you run %%GitHub%%) you'll first need to sign in with your account, then click Tools > Options. Set the "​Default Storage Directory"​ to something reasonable such as %%D:​\My_Documents\GitHub\%%). Also check that your username and e-mail address look ok (I am ''​mvdm''​). Next, configure your client. For %%GitHub%% Windows, after starting up the %%GitHub%% %%GUI%% (the default window that opens when you run %%GitHub%%) you'll first need to sign in with your account, then click Tools > Options. Set the "​Default Storage Directory"​ to something reasonable such as %%D:​\My_Documents\GitHub\%%). Also check that your username and e-mail address look ok (I am ''​mvdm''​).
Line 81: Line 83:
 === Using GitHub to acquire the FieldTrip toolbox === === Using GitHub to acquire the FieldTrip toolbox ===
  
-Using your experience from the previous section, create a local clone of the [[https://​github.com/​fieldtrip/​fieldtrip|%%FieldTrip%% toolbox]]. If you are using the command line, make sure that you ''​cd''​ to your ''​GitHub''​ folder, i.e. that you are not within some other project such as ''​nsb2015'',​ before cloning. If things worked correctly you should have ''​fieldtrip''​ and ''​nsb2015''​ folders within your %%GitHub%% folder; **not** a ''​fieldtrip''​ folder within your ''​nsb2015''​ folder!+Using your experience from the previous section, create a local clone of the [[https://​github.com/​fieldtrip/​fieldtrip|FieldTrip toolbox]]. If you are using the command line, make sure that you ''​cd''​ to your ''​GitHub''​ folder, i.e. that you are not within some other project such as ''​nsb2015'',​ before cloning. If things worked correctly you should have ''​fieldtrip''​ and ''​nsb2015''​ folders within your %%GitHub%% folder; **not** a ''​fieldtrip''​ folder within your ''​nsb2015''​ folder!
  
 We will use this toolbox extensively for the analysis of local field potentials. Be aware that it is about 1.2GB! We will use this toolbox extensively for the analysis of local field potentials. Be aware that it is about 1.2GB!
Line 134: Line 136:
 The choice of the folder name ''​promoted''​ indicates that these are data folders for which preprocessing is completed. As explained further in Module 2, preprocessing typically includes the renaming of raw data files, annotation, spike sorting, and a few other steps. In general, it is useful to keep promoted data separate from data still in process. The choice of the folder name ''​promoted''​ indicates that these are data folders for which preprocessing is completed. As explained further in Module 2, preprocessing typically includes the renaming of raw data files, annotation, spike sorting, and a few other steps. In general, it is useful to keep promoted data separate from data still in process.
  
-If you cannot access the NS&B share, use a %%FTP%% client such as [[https://​filezilla-project.org/​|Filezilla]] to connect to the lab %%FTP%% server, ''​mvdmlab-nas1''​ (129.97.62.84). Configure your %%FTP%% client to require "​explicit %%FTP%% over %%TLS%%"​ and use ''​BIOL680''​ as username and password. ​+If you cannot access the NS&B share, use a %%FTP%% client such as [[https://​filezilla-project.org/​|Filezilla]] to connect to the lab %%FTP%% server ​at **129.170.31.15**, use the following login settings (FileZilla):
  
-Correct FileZilla configuration is the following:​ +{{ :analysis:nsb2015:d-datavault-info.png?600 |}}
- +
-{{ :analysis:course:ftp_config.png?600 |}}+
  
 If you cannot log in to the server, send me your IP address and I will enable access for you. If you cannot log in to the server, send me your IP address and I will enable access for you.
Line 186: Line 186:
 </​code>​ </​code>​
  
-You should see some interesting oscillations -- we will explore these in detail in upcoming modules. If you see this, you have successfully completed this module!+You should see some interesting oscillations -- we will explore these in detail in upcoming modules. If you see this, you have successfully completed this introductory ​module!
  
 {{ :​analysis:​nsb2014:​verify.png?​600 |}} {{ :​analysis:​nsb2014:​verify.png?​600 |}}
  
-=== Folder and file naming === 
- 
-FIXME 
  
 === For Mac/OS X users === === For Mac/OS X users ===
analysis/nsb2015/week1.txt · Last modified: 2018/07/07 10:19 (external edit)