Update 'README.md'

README.md

@@ -1,240 +1,240 @@
-# Thiele_attention_gratc_V1_V4_laminar
-
-Simultaneous recordings from rhesus macaque V1 and V4 during a selective attention task.
-
-These preprocessed data allow reproduction of the analyses and results reported in the paper "Top-down coordination of local cortical state during selective attention", van Kempen (2020) Neuron.
-Code can be found [here](https://gitlab.com/JvK/cortical-state-coordination).
-
-## Data organisation & files
-
-Data is organised by subject and recording date.
-The folder `data/processed` contains the files necessary to replicate the main results described in this article. 
-Output from the analyses and the pooled results will be stored in `data/analysed` and `data/population`, respectively.
-In each recording folder, you can find the following files: 
-
-```
-Thiele_attention_V1_V4_laminar_gratc
-│   LICENCE.txt
-│   README.md
-│   datacite.yml    
-│
-└─── data
-     │
-     └─── processed
-          │
-          └─── J
-          └─── T
-          └─── W
-               └─── 2016-01-21
-               │    └─── SNR.mat
-               │    └─── V1_Coordinates.mat
-               │    └─── V4_Coordinates.mat
-               │    └─── hash.mat
-               │    └─── pupil.mat
-               │    └─── rf.mat
-               │    └─── stability.mat
-               │    └─── trialdata.mat
-               │
-               └─── 2016-01-22
-               │    ...
-```
-
-- LFPb.mat : bipolar rereferenced local field potentials
-- SNR.mat : signal to noise ratios
-- V1_Coordinates/V4_Coordinates.mat : electrode depth coordinates
-- hash.mat : population spiking activity, thresholded such that each channel has approximately 100 Hz firing rate
-- pupil.mat : pupil diameter data
-- rf.mat : receptive field locations
-- stability.mat : info about which periods of the recording were stable
-- trialdata.mat : trial info, events and reaction times etc.
-
-
-
-## Files
-
-### Coordinates
-
-Electrode depth coordinates can be found in the files `V1_Coordinates.mat` and `V4_Coordinates.mat`.
-Each of these files is a matrix with 3 columns. 
-
-```Matlab
-Coordinates =
-
-   -0.9404   -6.0000    0.1500
-   -0.7904   -5.0000    0.3000
-   -0.6404   -4.0000    0.4500
-   -0.4904   -3.0000    0.6000
-   -0.3404   -2.0000    0.7500
-   -0.1904   -1.0000    0.9000
-   -0.0404         0    1.0500
-    0.1096    1.0000    1.2000
-    0.2596    2.0000    1.3500
-    0.4096    3.0000    1.5000
-    0.5596    4.0000    1.6500
-    0.7096    5.0000    1.8000
-    0.8596    6.0000    1.9500
-    1.0096    7.0000    2.1000
-    1.1596    8.0000    2.2500
-    1.3096    9.0000    2.4000
-```
-
-- The first column indicates the depth of the contact (in μm), relative to the alignment channel estimated as the input layer (layer IV). The first channel (`Coordinates(1,:)`) is the lowest channel and is inserted first (deepest into the tissue). Thus, the most negative numbers are deepest into the tissue.
-- The second column indicates the channel index relative to the alignment channel.
-- The third column indicates the electrode spacing (spaced 150 μm)
-
-### Hash
-
-Population activity was extracted by lower spike threshold such that average firing rates were approximately 100 Hz for each channel. This population activity is stored in `hash.mat`.
-Inside this file, you'll find the following variables:
-
-```matlab
-      FixAlign: {32×735 cell}      
-     StimAlign: {32×735 cell}
-      CueAlign: {32×735 cell}
-     Dim1Align: {32×735 cell}
-     Dim2Align: {32×735 cell}
-       numUnit: 32
-      unitList: [32×1 double]
-          area: [32×2 char]
-```
-
-The fields `...Align` are variables with the data aligned to each of the events. This is a cell array of size (number of channels $x$ number of trials). Each cell contains spike times relative to the event.
-The variable `unitList` contains the channel number and `area` contains which area a certain channel was recorded from. 
-
-### LFPb
-
-Bipolar re-referenced local field potential (LFP) activity is stored in `LFPb.mat`. This file contains: 
-```matlab
-  struct with fields:
-
-    CueAlign: [1×1 struct]
-          SF: 1017
-     numUnit: 30
-    unitList: [30×1 double]
-        area: [30×2 char]
-```
-
-The fields `...Align` are variables with the data aligned to each of the events. Each of these is a structure with the following fields:
-```matlab
-  struct with fields:
-
-    TimeStamps: [1×4069 double]
-       Samples: [30×376×4069 double]
-```
-`TimeStamps` is an array with the times relative to the event. `Samples` is a 3D array of size (number of channels $x$ number of trials $x$ number of time points).
-The variable `unitList` contains the channel number and `area` contains which area a certain channel was recorded from. Because of the bipolar re-referencing, there are 15 channels in each area (instead of 16). 
-
-### Pupil
-
-The file `pupil.mat` contains pupil diameter data, aligned to stimulus onset. Unfortunately, pupil diameter was not recorded for all recordings (75/83).
-
-```matlab
-StimAlign = 
-
-  struct with fields:
-
-    TimeStamps: [1×751 double]
-       Samples: [1×735×751 double]
-```
-
-### SNR
-
-The file `SNR.mat` contains the signal-to-noise ratios for each channel, based on the MUAe signal. The file contains only 1 variable:
-
-```matlab
-    SNR: [32×3 table]
-```
-
-The variable `SNR` contains a table with the channel number (unitList), the area and maximum signal-to-noise ratio (SNR) in any of the tested time windows for each channel.
-
-```matlab
-  32×3 table
-
-    unitList    area      SNR  
-    ________    ____    _______
-
-        1        V1      1.5658
-        2        V1        3.13
-        3        V1      13.076
-        4        V1      12.906
-        5        V1      26.571
-        6        V1      38.108
-        7        V1      45.913
-        8        V1      52.399
-        9        V1      96.766
-       10        V1      33.067
-       11        V1      34.225
-       12        V1      21.108
-       13        V1      11.472
-       14        V1       5.039
-       15        V1     0.86814
-       16        V1     0.53039
-       17        V4      36.337
-       18        V4      29.928
-       19        V4      28.666
-       20        V4      27.546
-       21        V4      16.787
-       22        V4      21.231
-       23        V4      12.358
-       24        V4      10.803
-       25        V4      9.4491
-       26        V4       11.73
-       27        V4      11.973
-       28        V4      10.374
-       29        V4      14.974
-       30        V4      4.3474
-       31        V4     0.99858
-       32        V4      0.1953
-```
-
-### Stability
-
-Recording stability (during the attention task) was determined by investigating possible drifts in the energy of the activity in the baseline period. The trial selection based on this criteria is stored in `stability.mat`. We selected the longest trial window that showed stable activity across all channels.
-
-```matlab
-    selectedTrialWindow: [354 674]
-           chan2exclude: [1×0 double]
-```
-In this particular recording, we selected a trial window between 354 and 674, stored in `selectedTrialWindow`. 
-The variable `chan2exclude` contains channels excluded from analyses.
-
-### Trialdata
-The file `trialdata.mat` contains the metadata about each trial, e.g. the condition number, the events, etc. 
-
-```matlab
-trialdata = 
-
-  1×803 struct array with fields:
-
-    eventArray
-    NLX_events
-    cond_num
-    RT_EPP
-    targetDim
-    rfDim
-    positionRF
-    positionOut1
-    positionOut2
-    fixbreak
-```
-
-- `eventArray`: the events as recorded by The Cortex 
-- `NLX_events`: the events as recorded by Cheetah (Neuralynx)
-- `cond_num`: the condition number (1 & 4 for attend RF, 2 & 5 for attend away 1, 3 & 6 for attend away 2)
-- `RT_EPP`: the reaction time
-- `targetDim`: during which 'dimmming event' (first, second or third) the target changed luminance
-- `rfDim`: during which 'dimmming event' (first, second or third) changed the grating inside the receptive field (RF) in luminance
-- `positionRF`: position of grating inside RF
-- `positionOut1`: position of first grating outside RF
-- `positionOut2`: position of second grating outside RF
-- `fixbreak`: boolean indicating whether fixbreak occurred on this trial
-
-## Funding
-
-- Wellcome trust, 093104 
-- MRC, MR/P013031/1
-
-## Credits
-
-- Data collection: Jochem van Kempen and Michael Boyd in the lab of Alexander Thiele, Newcastle University, UK
+# Thiele_attention_gratc_V1_V4_laminar
+
+Simultaneous recordings from rhesus macaque V1 and V4 during a selective attention task.
+
+These preprocessed data allow reproduction of the main analyses and results reported in the paper "Top-down coordination of local cortical state during selective attention", van Kempen (2020) BioRxiv ([doi: 10.1101/2020.03.26.009365](https://www.biorxiv.org/content/10.1101/2020.03.26.009365v1)).  
+Code can be found [here](https://gitlab.com/JvK/cortical-state-coordination).
+
+## Data organisation & files
+
+Data is organised by subject and recording date.
+The folder `data/processed` contains the files necessary to replicate the main results described in this article. 
+Output from the analyses and the pooled results will be stored in `data/analysed` and `data/population`, respectively.
+
+### Files
+In each recording folder, you can find the following files: 
+
+```
+Thiele_attention_V1_V4_laminar_gratc
+│   LICENCE.txt
+│   README.md
+│   datacite.yml    
+│
+└─── data
+     │
+     └─── processed
+          │
+          └─── J
+          └─── T
+          └─── W
+               └─── 2016-01-21
+               │    └─── LFPb.mat
+               │    └─── SNR.mat
+               │    └─── V1_Coordinates.mat
+               │    └─── V4_Coordinates.mat
+               │    └─── hash.mat
+               │    └─── pupil.mat
+               │    └─── rf.mat
+               │    └─── stability.mat
+               │    └─── trialdata.mat
+               │
+               └─── 2016-01-22
+               │    ...
+```
+
+- LFPb.mat : bipolar rereferenced local field potentials
+- SNR.mat : signal to noise ratios
+- V1_Coordinates/V4_Coordinates.mat : electrode depth coordinates
+- hash.mat : population spiking activity, thresholded such that each channel has approximately 100 Hz firing rate
+- pupil.mat : pupil diameter data
+- rf.mat : receptive field locations
+- stability.mat : info about which periods of the recording were stable
+- trialdata.mat : trial info, events and reaction times etc.
+
+
+### Coordinates
+
+Electrode depth coordinates can be found in the files `V1_Coordinates.mat` and `V4_Coordinates.mat`.
+Each of these files is a matrix with 3 columns. 
+
+```Matlab
+Coordinates =
+
+   -0.9404   -6.0000    0.1500
+   -0.7904   -5.0000    0.3000
+   -0.6404   -4.0000    0.4500
+   -0.4904   -3.0000    0.6000
+   -0.3404   -2.0000    0.7500
+   -0.1904   -1.0000    0.9000
+   -0.0404         0    1.0500
+    0.1096    1.0000    1.2000
+    0.2596    2.0000    1.3500
+    0.4096    3.0000    1.5000
+    0.5596    4.0000    1.6500
+    0.7096    5.0000    1.8000
+    0.8596    6.0000    1.9500
+    1.0096    7.0000    2.1000
+    1.1596    8.0000    2.2500
+    1.3096    9.0000    2.4000
+```
+
+- The first column indicates the depth of the contact (in μm), relative to the alignment channel estimated as the input layer (layer IV). The first channel (`Coordinates(1,:)`) is the lowest channel and is inserted first (deepest into the tissue). Thus, the most negative numbers are deepest into the tissue.
+- The second column indicates the channel index relative to the alignment channel.
+- The third column indicates the electrode spacing (spaced 150 μm)
+
+### Hash
+
+Population activity (hash) was extracted by lowering the spiking threshold such that average firing rates were approximately 100 Hz for each channel. This population activity is stored in `hash.mat`.
+Inside this file, you'll find the following variables:
+
+```matlab
+      FixAlign: {32×735 cell}      
+     StimAlign: {32×735 cell}
+      CueAlign: {32×735 cell}
+     Dim1Align: {32×735 cell}
+     Dim2Align: {32×735 cell}
+       numUnit: 32
+      unitList: [32×1 double]
+          area: [32×2 char]
+```
+
+The fields `...Align` are variables with the data aligned to each of the events. This is a cell array of size (number of channels × number of trials). Each cell contains spike times relative to the event.
+The variable `unitList` contains the channel number and `area` contains which area a certain channel was recorded from. 
+
+### LFPb
+
+Bipolar re-referenced local field potential (LFP) activity is stored in `LFPb.mat`. This file contains: 
+```matlab
+  struct with fields:
+
+    CueAlign: [1×1 struct]
+          SF: 1017
+     numUnit: 30
+    unitList: [30×1 double]
+        area: [30×2 char]
+```
+
+The fields `...Align` are variables with the data aligned to each of the events. Each of these is a structure with the following fields:
+```matlab
+  struct with fields:
+
+    TimeStamps: [1×4069 double]
+       Samples: [30×376×4069 double]
+```
+`TimeStamps` is an array with the times relative to the event. `Samples` is a 3D array of size (number of channels × number of trials × number of time points).
+The variable `unitList` contains the channel number and `area` contains which area a certain channel was recorded from. Because of the bipolar re-referencing, there are 15 channels in each area (instead of 16). 
+
+### Pupil
+
+The file `pupil.mat` contains pupil diameter data, aligned to stimulus onset. Pupil diameter was recorded for most recordings (75/83).
+
+```matlab
+StimAlign = 
+
+  struct with fields:
+
+    TimeStamps: [1×751 double]
+       Samples: [1×735×751 double]
+```
+
+### SNR
+
+The file `SNR.mat` contains the signal-to-noise ratios for each channel, based on the MUAe signal. The file contains only 1 variable:
+
+```matlab
+    SNR: [32×3 table]
+```
+
+The variable `SNR` contains a table with the channel number (unitList), the area and maximum signal-to-noise ratio (SNR) in any of the tested time windows for each channel.
+
+```matlab
+  32×3 table
+
+    unitList    area      SNR  
+    ________    ____    _______
+
+        1        V1      1.5658
+        2        V1        3.13
+        3        V1      13.076
+        4        V1      12.906
+        5        V1      26.571
+        6        V1      38.108
+        7        V1      45.913
+        8        V1      52.399
+        9        V1      96.766
+       10        V1      33.067
+       11        V1      34.225
+       12        V1      21.108
+       13        V1      11.472
+       14        V1       5.039
+       15        V1     0.86814
+       16        V1     0.53039
+       17        V4      36.337
+       18        V4      29.928
+       19        V4      28.666
+       20        V4      27.546
+       21        V4      16.787
+       22        V4      21.231
+       23        V4      12.358
+       24        V4      10.803
+       25        V4      9.4491
+       26        V4       11.73
+       27        V4      11.973
+       28        V4      10.374
+       29        V4      14.974
+       30        V4      4.3474
+       31        V4     0.99858
+       32        V4      0.1953
+```
+
+### Stability
+
+Recording stability (during the attention task) was determined by investigating possible drifts in the energy of the activity in the baseline period. The trial selection based on this criteria is stored in `stability.mat`. We selected the longest trial window that showed stable activity across all channels.
+
+```matlab
+    selectedTrialWindow: [354 674]
+           chan2exclude: [1×0 double]
+```
+In this particular recording, we selected a trial window between 354 and 674, stored in `selectedTrialWindow`. 
+The variable `chan2exclude` contains channels excluded from analyses.
+
+### Trialdata
+The file `trialdata.mat` contains the metadata about each trial, e.g. the condition number, the events, etc. 
+
+```matlab
+trialdata = 
+
+  1×803 struct array with fields:
+
+    eventArray
+    NLX_events
+    cond_num
+    RT_EPP
+    targetDim
+    rfDim
+    positionRF
+    positionOut1
+    positionOut2
+    fixbreak
+```
+
+- `eventArray`: the events as recorded by The Cortex 
+- `NLX_events`: the events as recorded by Cheetah (Neuralynx)
+- `cond_num`: the condition number (1 & 4 for attend RF, 2 & 5 for attend away 1, 3 & 6 for attend away 2)
+- `RT_EPP`: the reaction time
+- `targetDim`: during which 'dimmming event' (first, second or third) the target changed luminance
+- `rfDim`: during which 'dimmming event' (first, second or third) changed the grating inside the receptive field (RF) in luminance
+- `positionRF`: position of grating inside RF
+- `positionOut1`: position of first grating outside RF
+- `positionOut2`: position of second grating outside RF
+- `fixbreak`: boolean indicating whether fixbreak occurred on this trial
+
+## Funding
+
+- Wellcome trust, 093104 
+- MRC, MR/P013031/1
+
+## Credits
+
+- Data collection: Jochem van Kempen and Michael Boyd in the lab of Alexander Thiele, Newcastle University, UK
 - Data processing: Jochem van Kempen, Michael Boyd and Demetrio Ferro