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analysis:adrlab [2013/08/09 13:24]
aacarey [Basic data loading]
analysis:adrlab [2018/07/07 10:19]
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-===== Overview of data files ===== 
  
-A promoted (i.e. pre-processed,​ annotated, and approved) data folder consists of most of the following files: 
- 
-   * *.Ncs files: continuously sampled data, "local field potentials"​ 
-   * (*.ntt files: raw tetrode files, these are generally not included) 
-   * *.Nev file: raw Events file 
-   * *.Nvt file: video tracking file (usually zipped) 
- 
-The above are raw data files stored by Neuralynx. The following files are the result of preprocessing and annotation: 
- 
-   * *.t files: spike times for one putative neuron (output from MClust) 
-   * *.clusters: cluster information (output from MClust, you will generally not need this) 
-   * *wv.mat and *%%ClusterQual%%.mat files: waveforms and cluster quality metrics 
-   * *Metadata.mat file: structured task-related information such as locations of feeders, times of rewards, etc. (not included in all sessions) 
-   * *%%ExpKeys%%.m file: basic information about this recording session, such as task, start time, end time, etc. (note this is a .m file, so needs to be run rather than loaded as you would a .mat file) 
-   * *vt.mat file: pre-processed video tracking data 
- 
-Note the naming convention for the above files: all files are identified by the RYYYY-MM-DD string in the filename, and recording files are further named with the tetrode number. 
- 
-===== Basic data loading ===== 
- 
-The below will only work if you have grabbed the vandermeerlab code base and added it to your MATLAB path ([[computing:​matlabsetup|instructions]]). If you are using a Mac, you will need to get the data loading files from Neuralynx and add them to the relevant folders (you'​ll know where when you get errors upon trying to load something). 
- 
-First, change your current (working) folder to the recording session of interest. 
- 
-Spike time series from a single cluster (putative neuron) are stored in a *.t file. These files are generated by MClust after the spike sorting process is complete. 
- 
-To load all spike trains in a folder: 
- 
-<code matlab> 
->> S = LoadSpikes(FindFiles('​*.t'​));​ 
-</​code>​ 
- 
-this gives a cell array S with one cell for each spike train, stored in a ts object: 
- 
-<code matlab> 
->> plot(Data(S{1}),​0,'​.k'​);​ % crude plot 
-</​code>​ 
- 
-This plots the spike times of the first cluster. A ts object is a custom (not built in into MATLAB) object with a number of methods (functions):​ the most useful are Data (get the spike times stored in it) and Restrict (restrict the spike times to specific times). 
- 
-To load and plot a CSC file: 
- 
-<code matlab> 
->> csc = LoadCSC(FindFile('​*CSC1a.Ncs'​),'​ConvertToS',​1);​ 
->> plot(Range(csc),​Data(csc));​ 
-</​code>​ 
- 
-Note that %%LoadCSC%% returns a tsd object ("​timestamped data") which consists of matching arrays of times and data. As with ts objects, Range() returns the times, but now there is also Data() which returns the data. 
- 
-Be aware that this time series can be restricted to the time the rat was actually freely moving and engaged in behavior; use the %%ExpKeys%% file and the Restrict function explained below to do this. 
- 
-To access the position data, first load the *vt.mat file (which contains the x and y tsd objects) and then do: 
- 
-<code matlab> 
-x_data = Data(Vt.x); 
-y_data = Data(Vt.y); 
-plot(x_data,​y_data,'​.'​);​ % notice this has some extra tracking data outside of the track 
-</​code>​ 
- 
-We will now use the %%ExpKeys%% file and Restrict to only include data when the rat was actually on the track: 
- 
-<code matlab> 
-run(FindFile('​*keys.m'​));​ % load experimental metadata; notice this is a script so we can run it 
-x = Restrict(Vt.x,​ExpKeys.TimeOnTrack,​ExpKeys.TimeOffTrack);​ % only include data from when rat was on track 
-y = Restrict(Vt.y,​ExpKeys.TimeOnTrack,​ExpKeys.TimeOffTrack);​ 
-plot(Data(x),​Data(y),'​.'​);​ % looks better now 
-</​code>​ 
- 
- 
-====== Description of the Multiple-T task ====== 
- 
- 
-====== ExpKeys ====== 
- 
-====== Metadata ====== 
- 
-This is example of a Metadata struct, taken from session ZXXX 
- 
-<code matlab> 
->> Metadata 
- 
-Metadata =  
- 
-         ​Feeders:​ {[1x1 struct] ​ [1x1 struct] ​ [1x1 struct] ​ [1x1 struct]} 
-          Events: {[1x1 struct] ​ [1x1 struct] ​ [1x1 struct]} 
-     ​TimeOnTrack:​ 627.5610 
-    TimeOffTrack:​ 3.0261e+03 
-      SwitchTime: 1.7264e+03 
-        goodFood: '​y'​ 
-         ​Markers:​ [1x1 struct] 
-         ​Linpath:​ [1x1 struct] 
-</​code>​ 
analysis/adrlab.txt ยท Last modified: 2018/07/07 10:19 (external edit)