From 32aac04b758a17527f49cdd854d60b93d1c01e86 Mon Sep 17 00:00:00 2001
From: Ceren <battal.ceren@gmail.com>
Date: Tue, 4 Aug 2020 10:14:50 +0100
Subject: [PATCH 1/5] typo fix

---
 README.md | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index 5a008fdc..eff43c91 100644
--- a/README.md
+++ b/README.md
@@ -36,7 +36,7 @@ Subjects, session and run number labels will be numbers with zero padding up to
 
 A session folder will ALWAYS be created even if not requested (default will be `ses-001`).
 
-Task labels will be printed in camelCase in the filenames. 
+Task labels will be printed in camelCase in the filenames.
 
 Time stamps are added directly in the filename by adding a suffix `_date-YYYYMMDDHHMM` which makes the file name non-BIDS compliant. This was added to prevent overwriting files in case a certain run needs to be done a second time because of a crash (Some of us are paranoid about keeping even cancelled runs during my experiments). This suffix should be removed to make the data set BIDS compliant. See `convertSourceToRaw.m` for more details.
 
@@ -206,7 +206,7 @@ For the moment the date of acquisition is appended to the filename
 
 Function to save output files for events that will be BIDS compliant.
 
-If the user DOES NOT provide `onset`, `trial_type`, this events will be skipped. `duration` will be set to "NaN" if 
+If the user DOES NOT provide `onset`, `trial_type`, this events will be skipped. `duration` will be set to "NaN" if
 no value is provided.
 
 ### checkCFG
@@ -216,7 +216,7 @@ Check that we have all the fields that we need in the experiment parameters.
 ## CFG content
 
 ```matlab
-%% Can be modified by users 
+%% Can be modified by users
 % but their effect might only be effective after running
 % checkCFG
 
@@ -290,7 +290,7 @@ cd fullpath_to_directory_where_to_install
 # use git to download the code
 git clone https://github.com/cpp-lln-lab/CPP_BIDS.git
 # move into the folder you have just created
-cd CPP_PTB
+cd CPP_BIDS
 # add the src folder to the matlab path and save the path
 matlab -nojvm -nosplash -r "addpath(fullfile(pwd, 'src')); savepath ();"
 ```
@@ -316,18 +316,18 @@ cd fullpath_to_directory_where_to_install
 # use git to download the code
 git submodule add https://github.com/cpp-lln-lab/CPP_BIDS.git
 # move into the folder you have just created
-cd CPP_PTB
+cd CPP_BIDS
 # add the src folder to the matlab path and save the path
 matlab -nojvm -nosplash -r "addpath(fullfile(pwd, 'src'))"
 ```
 
-To get the latest commit you then need to update the submodule with the information 
+To get the latest commit you then need to update the submodule with the information
 on its remote repository and then merge those locally.
 ```bash
 git submodule update --remote --merge
 ```
 
-Remember that updates to submodules need to be commited as well. 
+Remember that updates to submodules need to be commited as well.
 
 **TO DO**
 <!-- Submodules

From d4ca2f0825f69e68cd4e6890a8c8a557108e14f2 Mon Sep 17 00:00:00 2001
From: Ceren <battal.ceren@gmail.com>
Date: Tue, 4 Aug 2020 10:58:44 +0100
Subject: [PATCH 2/5] suggestion for submodule example

---
 README.md | 27 ++++++++++++++++++++++++++-
 1 file changed, 26 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index eff43c91..60370058 100644
--- a/README.md
+++ b/README.md
@@ -327,7 +327,32 @@ on its remote repository and then merge those locally.
 git submodule update --remote --merge
 ```
 
-Remember that updates to submodules need to be commited as well.
+Remember that updates to submodules need to be committed as well.
+
+#### Example for submodule usage
+
+So say you want to clone a repo that has some nested submodules, then you would type this to get the content of all the submodules at once (here with assumption that you want to clone my experiment repo):
+``` bash
+git clone --recurse-submodules https://github.com/user_name/myExperiment.git
+```
+This would be the way to do it fast way.
+
+To do it in more controlled/slow motion, see below
+```bash
+# clone the repo
+git clone https://github.com/user_name/myExperiment.git
+
+# go into the directory
+cd myExperiment
+
+# initialize and get the content of the first level of submodules  (e.g. CPP_PTB and CPP_BIDS)
+git submodule init
+git submodule update
+
+# get the nested submodules JSONio and BIDS-matlab for CPP_BIDS
+git submodule foreach --recursive 'git submodule init'
+git submodule foreach --recursive 'git submodule update'
+```
 
 **TO DO**
 <!-- Submodules

From 7e851ed3b60e9c4f9322e47af2f36ccb769aecae Mon Sep 17 00:00:00 2001
From: Ceren <battal.ceren@gmail.com>
Date: Tue, 4 Aug 2020 11:28:54 +0100
Subject: [PATCH 3/5] fix for nested submodule

---
 README.md | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/README.md b/README.md
index 60370058..e2bed3bf 100644
--- a/README.md
+++ b/README.md
@@ -332,12 +332,6 @@ Remember that updates to submodules need to be committed as well.
 #### Example for submodule usage
 
 So say you want to clone a repo that has some nested submodules, then you would type this to get the content of all the submodules at once (here with assumption that you want to clone my experiment repo):
-``` bash
-git clone --recurse-submodules https://github.com/user_name/myExperiment.git
-```
-This would be the way to do it fast way.
-
-To do it in more controlled/slow motion, see below
 ```bash
 # clone the repo
 git clone https://github.com/user_name/myExperiment.git

From 442eec11cbcc414305c3dab150883d4559191a91 Mon Sep 17 00:00:00 2001
From: Ceren <battal.ceren@gmail.com>
Date: Tue, 4 Aug 2020 11:39:25 +0100
Subject: [PATCH 4/5] cfg.task name correction

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index e2bed3bf..687c84cc 100644
--- a/README.md
+++ b/README.md
@@ -56,7 +56,7 @@ sub-090/ses-003/sub-090_ses-003_task-auditoryTask_run-023_events_date-2020072915
 cfg.outputDir = fullfile(pwd, '..', 'output');
 
 % define the name of the task
-cfg.task = 'test task';
+cfg.task.name = 'test task';
 
 % can use the userInputs function to collect subject info
 % cfg = userInputs;
@@ -111,7 +111,7 @@ If you want to save more complex events.tsv file you can save several columns at
 ```matlab
 cfg.subjectNb = 1;
 cfg.runNb = 1;
-cfg.task = 'testtask';
+cfg.task.name = 'testtask';
 cfg.outputDir = outputDir;
 
 cfg.testingDevice = 'mri';

From 41cc9eebe916c887a6ca3e324fff10134c95fc26 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Tue, 4 Aug 2020 12:47:30 +0200
Subject: [PATCH 5/5] fix field info about subject and run number

---
 README.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 687c84cc..c840bb0c 100644
--- a/README.md
+++ b/README.md
@@ -62,8 +62,8 @@ cfg.task.name = 'test task';
 % cfg = userInputs;
 
 % or declare it directly
-cfg.subjectNb = 1;
-cfg.runNb = 1;
+cfg.subject.subjectNb = 1;
+cfg.subject.runNb = 1;
 
 % by default we assume you are running things on a behavioral PC with no eyetracker
 % cfg.eyeTracker = false;
@@ -109,8 +109,8 @@ saveEventsFile('close', cfg, logFile);
 If you want to save more complex events.tsv file you can save several columns at once.
 
 ```matlab
-cfg.subjectNb = 1;
-cfg.runNb = 1;
+cfg.subject.subjectNb = 1;
+cfg.subject.runNb = 1;
 cfg.task.name = 'testtask';
 cfg.outputDir = outputDir;