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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.
Subjects, session and run number labels will be numbers with zero padding up to 3 values (e.g subject 1 will become `sub-001`).
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Subjects, session and run number labels will be numbers with zero padding up to
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3 values (e.g subject 1 will become `sub-001`).
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A session folder will ALWAYS be created even if not requested (default will be `ses-001`).
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A session folder will ALWAYS be created even if not requested (default will be
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`ses-001`).
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Task labels will be printed in camelCase in the filenames.
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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.
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Time stamps are added directly in the filename by adding a suffix
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`_date-YYYYMMDDHHMM` which makes the file name non-BIDS compliant. This was
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added to prevent overwriting files in case a certain run needs to be done a
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second time because of a crash (Some of us are paranoid about keeping even
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cancelled runs during my experiments). This suffix should be removed to make the
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data set BIDS compliant. See `convertSourceToRaw.m` for more details.
This function creates a very light-weight version of the side-car JSON file for a BOLD functional run.
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This function creates a very light-weight version of the side-car JSON file for
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a BOLD functional run.
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This will only contain the minimum BIDS requirement and will likely be less complete than the info you could from DICOM conversion.
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This will only contain the minimum BIDS requirement and will likely be less
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complete than the info you could from DICOM conversion.
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If you put the following line at the end of your experiment script, it will dump the content of the `extraInfo` structure in the json file.
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If you put the following line at the end of your experiment script, it will dump
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the content of the `extraInfo` structure in the json file.
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```
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createBoldJson(cfg, extraInfo)
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```
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This allows to add all the parameters that you used to run your experiment in a human readable format: so that when you write your methods sections 2 years later ("the reviewer asked me for the size of my fixation cross... FML"), the info you used WHEN you ran the experiment is saved in an easily accessible text format. For the love of the flying spaghetti monster do not save all your parameters in a `.mat` file: think of the case when you won't have matlab or octave installed on a computer (plus not everyone uses those).
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Also to reading your experiment parameters, you won't have to read it from the `setParameters.m` file and wonder if those might have been modified when running the experiment and you did not commit and tagged that change with git.
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This allows to add all the parameters that you used to run your experiment in a
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human readable format: so that when you write your methods sections 2 years
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later ("the reviewer asked me for the size of my fixation cross... FML"), the
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info you used WHEN you ran the experiment is saved in an easily accessible text
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format. For the love of the flying spaghetti monster do not save all your
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parameters in a `.mat` file: think of the case when you won't have matlab or
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octave installed on a computer (plus not everyone uses those).
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Also to reading your experiment parameters, you won't have to read it from the
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`setParameters.m` file and wonder if those might have been modified when running
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the experiment and you did not commit and tagged that change with git.
To get the latest commit you then need to update the submodule with the information
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on its remote repository and then merge those locally.
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To get the latest commit you then need to update the submodule with the
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information on its remote repository and then merge those locally.
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```bash
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git submodule update --remote --merge
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```
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Remember that updates to submodules need to be committed as well.
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### 2.1. <aname='Exampleforsubmoduleusage'></a>Example for submodule usage
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### 2.1. <aname='Exampleforsubmoduleusage'></a>Example for submodule usage
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So say you want to clone a repo that has some nested submodules, then you would
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type this to get the content of all the submodules at once (here with assumption
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that you want to clone my experiment repo):
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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):
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