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Merged
merged 7 commits into from
Aug 4, 2020
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submodule example modification #67

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c431350
Merge remote-tracking branch 'cpp-lln-lab/master'
CerenB Aug 3, 2020
17f9d1e
Merge remote-tracking branch 'cpp-lln-lab/master'
CerenB Aug 4, 2020
32aac04
typo fix
CerenB Aug 4, 2020
d4ca2f0
suggestion for submodule example
CerenB Aug 4, 2020
7e851ed
fix for nested submodule
CerenB Aug 4, 2020
442eec1
cfg.task name correction
CerenB Aug 4, 2020
41cc9ee
fix field info about subject and run number
Remi-Gau Aug 4, 2020
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45 changes: 32 additions & 13 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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.

Expand All @@ -56,14 +56,14 @@ 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;

% 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;
Expand Down Expand Up @@ -109,9 +109,9 @@ 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.task = 'testtask';
cfg.subject.subjectNb = 1;
cfg.subject.runNb = 1;
cfg.task.name = 'testtask';
cfg.outputDir = outputDir;

cfg.testingDevice = 'mri';
Expand Down Expand Up @@ -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
Expand All @@ -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

Expand Down Expand Up @@ -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 ();"
```
Expand All @@ -316,18 +316,37 @@ 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 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
# 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
Expand Down