Skip to content

Commit 5b62759

Browse files
Remi-GauRemi-Gau
committed
reorder readme
1 parent 14f58e4 commit 5b62759

File tree

1 file changed

+98
-114
lines changed

1 file changed

+98
-114
lines changed

‎README.md

Lines changed: 98 additions & 114 deletions
Original file line numberDiff line numberDiff line change
@@ -5,74 +5,69 @@
55

66
A set of function for matlab and octave to create [BIDS-compatible](https://bids-specification.readthedocs.io/en/stable/) folder structure and filenames for the output of behavioral, EEG, fMRI, eyetracking studies.
77

8-
Here are the naming templates used.
9-
10-
- BOLD
11-
12-
`sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]`
13-
14-
- iEEG
15-
16-
`sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_ieeg.json`
17-
18-
- EEG
19-
20-
`sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.<manufacturer_specific_extension>`
21-
22-
- Eyetracker
8+
## Usage
239

24-
`sub-<participant_label>[_ses-<label>][_acq-<label>]_task-<task_label>_eyetrack.<manufacturer_specific_extension>`
10+
```matlab
2511
26-
## Contributing
12+
% define the folder where the data will be saved
13+
expParameters.outputDir = fullfile(pwd, '..', 'output');
2714
28-
Feel free to open issues to report a bug and ask for improvements.
15+
% define the name of the task
16+
expParameters.task = 'testtask';
2917
30-
### Guidestyle
18+
% can use the userInputs function to collect subject info
19+
% expParameters = userInputs;
3120
32-
- We use camelCase.
33-
- We keep the McCabe complexity as reported by the [check_my_code function](https://github.com/Remi-Gau/matlab_checkcode) below 15.
21+
% or declare it directly
22+
expParameters.subjectGrp = '';
23+
expParameters.subjectNb = 1;
24+
expParameters.sessionNb = 1;
25+
expParameters.runNb = 1;
3426
35-
## How to install
27+
% Use the verbose switch to know where your data is being saved
28+
expParameters.verbose = true;
3629
37-
### Use the matlab package manager
30+
% In case you are using en eyetracker
31+
cfg.eyeTracker = false;
3832
39-
This repository can be added as a dependencies by listing it in a [mpm-requirements.txt file](.mpm-requirements.txt)
40-
as follows:
33+
% if the device is set to 'PC' then the data will be saved
34+
% in the `beh` folder
35+
cfg.device = 'PC';
4136
42-
```
43-
CPP_BIDS -u https://github.com/cpp-lln-lab/CPP_BIDS.git
44-
```
37+
% if the device is set to 'scanner' then the data will be saved
38+
% in the `func` folder
39+
% cfg.device = 'scanner';
4540
46-
You can then use the [matlab package manager](https://github.com/mobeets/mpm), to simply download the appropriate version of those dependencies and add them to your path by running a `getDependencies` function like the one below where you just need to replace `YOUR_EXPERIMENT_NAME` by the name of your experiment.
41+
% check that cfg and exparameters have all the necessary information
42+
% and fill in any missing field
43+
expParameters = checkCFG(cfg, expParameters);
4744
45+
% create the filenames
46+
expParameters = createFilename(cfg, expParameters);
4847
49-
```matlab
50-
function getDependencies(action)
51-
% Will install on your computer the matlab dependencies specified in the mpm-requirements.txt
52-
% and add them to the matlab path. The path is never saved so you need to run getDependencies() when
53-
% you start matlab.
54-
%
55-
% getDependencies('update') will force the update and overwrite previous version of the dependencies.
56-
%
57-
% getDependencies() If you only already have the appropriate version but just want to add them to the matlab path.
48+
% initialize the events files with the typical BIDS
49+
% columns (onsets, duration, trial_type)
50+
% and add some more in this case (Speed and is_Fixation)
51+
logFile = saveEventsFile('open', expParameters, [], 'Speed', 'is_Fixation');
5852
59-
experimentName = YOUR_EXPERIMENT_NAME;
53+
% create the information about 2 events that we want to save
54+
logFile(1,1).onset = 2;
55+
logFile(1,1).trial_type = 'motion_up';
56+
logFile(1,1).duration = 1;
57+
logFile(1,1).speed = 2;
58+
logFile(1,1).is_fixation = true;
6059
61-
if nargin<1
62-
action = '';
63-
end
60+
logFile(2,1).onset = 3;
61+
logFile(2,1).trial_type = 'static';
62+
logFile(2,1).duration = 4;
63+
logFile(2,1).is_fixation = 3;
6464
65-
switch action
66-
case 'update'
67-
% install dependencies
68-
mpm install -i mpm-requirements.txt -f -c YOUR_EXPERIMENT_NAME
69-
end
65+
% add those 2 events to the events.tsv file
66+
saveEventsFile('save', expParameters, logFile, 'speed', 'is_fixation');
7067
71-
% adds them to the path
72-
mpm_folder = fileparts(which('mpm'));
73-
addpath(genpath(fullfile(mpm_folder, 'mpm-packages', 'mpm-collections', experimentName)));
68+
% close the file
69+
saveEventsFile('close', expParameters, logFile);
7470
75-
end
7671
```
7772

7873
## Functions descriptions
@@ -81,11 +76,10 @@ end
8176

8277
Get subject, run and session number and make sure they are positive integer values.
8378

84-
8579
### createFilename
8680

87-
Create the BIDS compliant directories and filenames (but not the files) for the behavioral output for this subject /
88-
session / run.
81+
Create the BIDS compliant directories and filenames (but not the files) for the behavioral
82+
output for this subject / session / run.
8983

9084
Will also create the right filename for the eye-tracking data file.
9185

@@ -98,89 +92,79 @@ For the moment the date of acquisition is appended to the filename
9892

9993
Function to save output files for events that will be BIDS compliant.
10094

101-
10295
### checkCFG
10396
Check that we have all the fields that we need in the experiment parameters.
10497

98+
## How to install
10599

106-
## Usage
100+
### Use the matlab package manager
107101

108-
```matlab
102+
This repository can be added as a dependencies by listing it in a
103+
[mpm-requirements.txt file](.mpm-requirements.txt) as follows:
109104

110-
% define the folder where the data will be saved
111-
expParameters.outputDir = fullfile(pwd, '..', 'output');
105+
```
106+
CPP_BIDS -u https://github.com/cpp-lln-lab/CPP_BIDS.git
107+
```
112108

113-
% define the name of the task
114-
expParameters.task = 'testtask';
109+
You can then use the [matlab package manager](https://github.com/mobeets/mpm), to simply download
110+
the appropriate version of those dependencies and add them to your path by running a
111+
`getDependencies` function like the one below where you just need to replace
112+
`YOUR_EXPERIMENT_NAME` by the name of your experiment.
115113

116-
% can use the userInputs function to collect subject info
117-
% expParameters = userInputs;
114+
```matlab
115+
function getDependencies(action)
116+
% Will install on your computer the matlab dependencies specified in the mpm-requirements.txt
117+
% and add them to the matlab path. The path is never saved so you need to run getDependencies() when
118+
% you start matlab.
119+
%
120+
% getDependencies('update') will force the update and overwrite previous version of the dependencies.
121+
%
122+
% getDependencies() If you only already have the appropriate version but just want to add them to the matlab path.
118123
119-
% or declare it directly
120-
expParameters.subjectGrp = '';
121-
expParameters.subjectNb = 1;
122-
expParameters.sessionNb = 1;
123-
expParameters.runNb = 1;
124+
experimentName = YOUR_EXPERIMENT_NAME;
124125
125-
% Use the verbose switch to know where your data is being saved
126-
expParameters.verbose = true;
126+
if nargin<1
127+
action = '';
128+
end
127129
128-
% In case you are using en eyetracker
129-
cfg.eyeTracker = false;
130+
switch action
131+
case 'update'
132+
% install dependencies
133+
mpm install -i mpm-requirements.txt -f -c YOUR_EXPERIMENT_NAME
134+
end
130135
131-
% if the device is set to 'PC' then the data will be saved in the `beh` folder
132-
cfg.device = 'PC';
136+
% adds them to the path
137+
mpm_folder = fileparts(which('mpm'));
138+
addpath(genpath(fullfile(mpm_folder, 'mpm-packages', 'mpm-collections', experimentName)));
133139
134-
% if the device is set to 'scanner' then the data will be saved in the `func` folder
135-
% cfg.device = 'scanner';
140+
end
141+
```
136142

137-
% check that cfg and exparameters have all the necessary information and fill in any missing field
138-
expParameters = checkCFG(cfg, expParameters);
143+
## Contributing
139144

140-
% create the filenames
141-
expParameters = createFilename(cfg, expParameters);
145+
Feel free to open issues to report a bug and ask for improvements.
142146

143-
% initialize the events files with the typical BIDS columns (onsets, duration, trial_type)
144-
% and add some more in this case (Speed and is_Fixation)
145-
logFile = saveEventsFile('open', expParameters, [], 'Speed', 'is_Fixation');
147+
### Guidestyle
146148

147-
% create the information about 2 events that we want to save
148-
logFile(1,1).onset = 2;
149-
logFile(1,1).trial_type = 'motion_up';
150-
logFile(1,1).duration = 1;
151-
logFile(1,1).speed = 2;
152-
logFile(1,1).is_fixation = true;
149+
- We use camelCase.
150+
- We keep the McCabe complexity as reported by the [check_my_code function](https://github.com/Remi-Gau/matlab_checkcode) below 15.
153151

154-
logFile(2,1).onset = 3;
155-
logFile(2,1).trial_type = 'static';
156-
logFile(2,1).duration = 4;
157-
logFile(2,1).is_fixation = 3;
152+
### BIDS naming convention
158153

159-
% add those 2 events to the events.tsv file
160-
saveEventsFile('save', expParameters, logFile, 'speed', 'is_fixation');
154+
Here are the naming templates used.
161155

162-
% close the file
163-
saveEventsFile('close', expParameters, logFile);
156+
- BOLD
164157

165-
```
158+
`sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]`
159+
160+
- iEEG
166161

167-
## Contributors ✨
162+
`sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_ieeg.json`
168163

169-
Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
164+
- EEG
170165

171-
<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
172-
<!-- prettier-ignore-start -->
173-
<!-- markdownlint-disable -->
174-
<table>
175-
<tr>
176-
<td align="center"><a href="https://github.com/CerenB"><img src="https://avatars1.githubusercontent.com/u/10451654?v=4" width="100px;" alt=""/><br /><sub><b>CerenB</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_BIDS/commits?author=CerenB" title="Code">💻</a> <a href="#design-CerenB" title="Design">🎨</a> <a href="https://github.com/cpp-lln-lab/CPP_BIDS/commits?author=CerenB" title="Documentation">📖</a></td>
177-
<td align="center"><a href="https://github.com/marcobarilari"><img src="https://avatars3.githubusercontent.com/u/38101692?v=4" width="100px;" alt=""/><br /><sub><b>marcobarilari</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_BIDS/commits?author=marcobarilari" title="Code">💻</a> <a href="#design-marcobarilari" title="Design">🎨</a> <a href="https://github.com/cpp-lln-lab/CPP_BIDS/commits?author=marcobarilari" title="Documentation">📖</a></td>
178-
<td align="center"><a href="https://remi-gau.github.io/"><img src="https://avatars3.githubusercontent.com/u/6961185?v=4" width="100px;" alt=""/><br /><sub><b>Remi Gau</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_BIDS/commits?author=Remi-Gau" title="Code">💻</a> <a href="#design-Remi-Gau" title="Design">🎨</a> <a href="https://github.com/cpp-lln-lab/CPP_BIDS/commits?author=Remi-Gau" title="Documentation">📖</a></td>
179-
</tr>
180-
</table>
166+
`sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.<manufacturer_specific_extension>`
181167

182-
<!-- markdownlint-enable -->
183-
<!-- prettier-ignore-end -->
184-
<!-- ALL-CONTRIBUTORS-LIST:END -->
168+
- Eyetracker
185169

186-
This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!
170+
`sub-<participant_label>[_ses-<label>][_acq-<label>]_task-<task_label>_eyetrack.<manufacturer_specific_extension>`

0 commit comments

Comments
 (0)