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[ENH] Add ezBIDS tutorial video and minor edits #120

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10 changes: 6 additions & 4 deletions docs/tutorial/ezBIDS.md
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# **ezBIDS Tutorial**

The page provides a simple tutorial for using [ezBIDS](https://brainlife.io/ezbids). The goal of this tutorial is to demonstrate how to use ezBIDS in order to convert raw imaging data to BIDS. For more in-depth information regarding the functionality and feature of ezBIDS, please refer to the [user documentation](https://brainlife.io/docs/using_ezBIDS/).
The page provides a simple tutorial for using [ezBIDS](https://brainlife.io/ezbids). The goal of this tutorial is to demonstrate how to use ezBIDS in order to convert raw imaging data to BIDS. For more in-depth information regarding the functionality and features of ezBIDS, please refer to the [user documentation](https://brainlife.io/docs/using_ezBIDS/).

Before we begin, we'll need some test data, which can be found [here](https://drive.google.com/drive/folders/18Y0SuSAevh2pu7Wuv3BFnbrLZNlVMeJr?usp=sharing). After a few minutes, the data will be downloaded to your Downloads folder, titled "ezBIDS_tutorial_data".

Expand Down Expand Up @@ -88,6 +88,8 @@ As you can see, we have a standard collection of MRI data and corresponding timi

Now, we are ready to use ezBIDS. All you need is a web browser (Chrome or Firefox preferred) and an internet connection. Copy and paste the ezBIDS URL (https://brainlife.io/ezbids) into your web browser.

For a companion video that follows this documentation, see our [ezBIDS tutorial video](https://youtu.be/L8rWA8qgnpo).

### 1. Homepage

Upon reaching the ezBIDS homepage, click "LOG IN/REGISTER" in the upper right part of the web page to sign into your brainlife.io account. If you do not have a brainlife.io account, you will be guided through a quick setup. This process is simple and meant for authentication purposes.
Expand All @@ -97,7 +99,7 @@ Upon reaching the ezBIDS homepage, click "LOG IN/REGISTER" in the upper right pa

### 2. Upload Imaging Data

Click the "Choose Files" button and select the `data` folder to upload the imaging data. We will upload the `logs` folder later.
Click the "Choose Files" (or "Browse") button and select the `data` folder to upload the imaging data. We will upload the `logs` folder later.

!!! note
The tutorial should be in your Downloads folder, titled "ezBIDS_tutorial_data".
Expand All @@ -106,7 +108,7 @@ This upload process may take a couple of minutes, depending on the strength of y

### 3. Dataset Description

This page allows you to specify information about the entire dataset. Notice how ezBIDS will autofill several fields for you. Required fields have been marked with a red asterisk, indicating that this information is absolutely needed to have a BIDS-compliant dataset. However, the information that ezBIDS provides may not always be appropriate, necessitating changes if you so choose. For example, the **Dataset Name** is specified as *Untitled*, which isn't very informative. Let's change that field instead to *myData*. Additionally, the **Authors** field is currently blank since ezBIDS couldn't determine that information, and it's not a required field for BIDS compliance. Let's click the **Authors field type our name (e.g. *John Doe*), and press the Return (or Enter) button on your keyboard. You are more than welcome to provide additional information on this page, but for this tutorial, we will move on by clicking the "Next" button at the bottom right side of the web page.
This page allows you to specify information about the entire dataset. Notice how ezBIDS will autofill several fields for you. Required fields have been marked with a red asterisk, indicating that this information is absolutely needed to have a BIDS-compliant dataset. However, the information that ezBIDS provides may not always be appropriate, necessitating changes if you so choose. For example, the **Dataset Name** is specified as *Untitled*, which isn't very informative. Let's change that field instead to *myDataset*. Additionally, the **Authors** field is currently blank since ezBIDS couldn't determine that information, and it's not a required field for BIDS compliance. Let's click the **Authors field type our name (e.g. *John Doe*), and press the Return (or Enter) button on your keyboard. You are more than welcome to provide additional information on this page, but for this tutorial, we will move on by clicking the "Next" button at the bottom right side of the web page.

### 4. Subjects and Sessions

Expand Down Expand Up @@ -136,7 +138,7 @@ Once all warnings (and errors) are resolved, you can proceed to the next page.

### 6. Events

We will now upload the timing files in the `logs` directory of our tutorial data. Simply click the "Select File" button and specify the `logs` directory (you will upload all contents in there) in your "ezBIDS_tutorial_data" folder. You will then see a list of header fields on the left (`Onset`, `Duration`, etc) with a corresponding drop-down menu. This is ezBIDS's way of asking you to specify which columns in the timing files correspond to the header fields on the left. For `Onset`, choose *tstart*, and for `Duration` choose *dur*. These two headers are the only required fields to proceed; the rest are optional and can be left empty for this tutorial.
We will now upload the timing files in the `logs` directory of our tutorial data. Simply click the "Select File(s)" (or "Browse") button and specify the `logs` directory (you will upload all contents in there) in your "ezBIDS_tutorial_data" folder. You will then see a list of header fields on the left (`Onset`, `Duration`, etc) with a corresponding drop-down menu. This is ezBIDS's way of asking you to specify which columns in the timing files correspond to the header fields on the left. For `Onset`, choose *tstart*, and for `Duration` choose *dur*. These two headers are the only required fields to proceed; the rest are optional and can be left empty for this tutorial.

### 7. Dataset Review

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8 changes: 5 additions & 3 deletions docs/using_ezBIDS.md
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# **ezBIDS User Documentation**

[ezBIDS](https://brainlife.io/ezbids) is a web-based BIDS conversion tool that requires neither installation, programming proficiency, nor knowledge of the Unix terminal and BIDS specification. The term BIDS is an acronym that stands for the [Brain Imaging Data Structure](https://bids-specification.readthedocs.io/en/stable/). More specifically, BIDS is a format for describing and organizing (primarily neuroimaging) data, greatly enhancing data sharing within the scientific community, as well as enabling access to a suite of processing and analysis tools that can be automatically executed on BIDS data, known as [BIDS apps](https://bids-apps.neuroimaging.io/). This tutorial describes how to use ezBIDS to easily convert imaging data to BIDS.
[ezBIDS](https://brainlife.io/ezbids) is a web-based BIDS conversion tool that requires neither installation, programming proficiency, nor knowledge of the Unix terminal and BIDS specification. The term BIDS is an acronym that stands for the [Brain Imaging Data Structure](https://bids-specification.readthedocs.io/en/stable/). More specifically, BIDS is a format for describing and organizing (primarily neuroimaging) data, greatly enhancing data sharing within the scientific community, as well as enabling access to a suite of processing and analysis tools that can be automatically executed on BIDS data, known as [BIDS apps](https://bids-apps.neuroimaging.io/). This documentation provides an in-depth description of ezBIDS's functionality for converting data to BIDS.

If you are new to ezBIDS and would like to see a simple use case of ezBIDS, please refer to the [ezBIDS tutorial](https://brainlife.io/docs/tutorial/ezBIDS).

## A Primer to ezBIDS

Expand Down Expand Up @@ -72,9 +74,9 @@ On this page, ezBIDS provides the subject (and session, if applicable) IDs of th

![Subjects/Sessions](./img/ezbids/Levitas_etal_figureS4_subjects_sessions.png)

### 5. Grouping data
### 5. Series Mapping

ezBIDS organizes all uploaded data into specific series and group IDs. This is an intermediate step, that ezBIDS uses to facilitate editing entire series (or groups) of data files. Say, you want to change all the files from a single subject so that all the files start with a specific subject ID, or say you want to change all the data that are anatomical to start with the prefix *anat*, ezBIDS allows you to do that by grouping data for you by subjects, series, etc.
ezBIDS organizes all uploaded data into specific series and group IDs (grouping data). This is an intermediate step, that ezBIDS uses to facilitate editing entire series (or groups) of data files. Say, you want to change all the files from a single subject so that all the files start with a specific subject ID, or say you want to change all the data that are anatomical to start with the prefix *anat*, ezBIDS allows you to do that by grouping data for you by subjects, series, etc.

![Series Mapping](./img/ezbids/Levitas_etal_figureS5_series_mapping_all.png)

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