Update using_ezBIDS.md

docs/using_ezBIDS.md

@@ -134,13 +134,21 @@ Once complete, two screens are presented. On the left is a Linux tree structure
 Once a BIDS-compliant dataset is generated, users can click on the blue "Download BIDS" button to download their zipped data to their local computer/server, and/or send their BIDS data to [OpenNeuro.org](https://openneuro.org/) or [brainlife.io](https://brainlife.io/about/). 
 
 !!! info Downloading non-BIDS compliant data
-    Users may still download their BIDS dataset (or upload it elsewhere) even if the bids-validator returns error(s); however, users should know that their dataset     is not fully BIDS-compliant and will need to be corrected at some point.
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+    Users may still download their BIDS dataset (or upload it elsewhere) even if the bids-validator returns error(s); however, users should know that their dataset is not fully BIDS-compliant and will need to be corrected at some point. 
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+Lastly, upon completing the BIDS mapping, ezBIDS automatically generates a configuration template JSON file (`ezBIDS_template.json`) that details all information and changes made during the current ezBIDS session. This template can be uploaded with subsequent data from the same study, which reduces the time spent editing the BIDS structure on subsequent uploads of imaging data. See [here](#additional-information) for additional information. 
+
 ---
+## Additional Information
 
 !!! info ezBIDS configuration templates
     ezBIDS creates templates for scanning sessions. Any scanning session processed using ezBIDS can become a template for future sessions. ezBIDS Templates can be reused to automatically load the BIDS mapping configuration a user has identified. Templates are helpful in the common situation where the same scanning protocol is used for multiple sessions. Often, researchers set up a scanning protocol and configure a series of scans to be acquired on multiple subjects across the duration of a research project. When the scans from the first subject are uploaded and processed via ezBIDS the researcher is effectively creating an ezBIDS Template, automatically. ezBIDS Templates are JSON files created every time a dataset is processed via ezBIDS. To use the template all the user has to do is download the template and upload the template with any new sessions acquired in the future. ezBIDS Templates can be reused for any number of datasets and reduce users' interaction with the ezBIDS graphical interface. More specifically, after ezBIDS has converted a dataset to BIDS, users have the option to download the file `ezBIDS_template.json`. This file contains all information, to map the DICOMs to BIDS, including user edits and modifications, from the ezBIDS session. This file can be uploaded with new datasets. When done so, the information in the file is applied to the new ezBIDS session, all the graphical interface fields are loaded with the information initially set by the user, reducing time spent on edits. If a dataset is uploaded with the wrong template, or if the template needs to be modified, the user has the option to overwrite the template uploaded and use ezBIDS as usual via the graphical interface. The configuration also enables many-to-one or one-to-many mapping, meaning that the `ezBIDS_template.json` information can pertain to a single subject but be applied to a current upload with multiple subjects or even sessions. The `ezBIDS_template.json` file can be renamed if desired, however, it needs to end in `ezBIDS_template.json` in order for ezBIDS to know what to look for. Uploading an `ezBIDS_template.json` file will not let ezBIDS run automatically from start to finish, the user's review and approval are judicious.
 
+!!! info ezBIDS errors and warnings
+    ![ezBIDS errors and warnings](./img/ezbids/ezBIDS_errors_warnings.png)
+
+    ezBIDS alerts users to BIDS validation errors and provides additional guidance to BIDS validation via custom warnings, to ensure BIDS compliance and to provide recommendations for improved curation of datasets. **Errors**. Marked by an “x” symbol (red). Errors identify details that prevent the dataset from being BIDS compliant, identical to BIDS validator errors. These are displayed in red and must be rectified by the user before proceeding. In the example, the task entity label is missing from the func/bold sequence, which is required by BIDS. ezBIDS therefore flags it as an error to alert the user that this must be addressed. **Warnings**. Marked by an “!” symbol (gold). Warnings offer recommended changes to the current BIDS structure that would improve the quality and curation of the dataset, and are displayed in dark yellow. Unlike errors, ezBIDS warnings are different from the BIDS validator warnings; ezBIDS warnings are unique recommendations presented to users as a way to improve the quality of details and metadata that the final BIDS datasets will be stored with. In the example, the user specifies the phase encoding direction (direction) entity label as “PA”, when in reality, ezBIDS knows that the correct label should be “AP”. Such warnings alert users to potential mistakes that might overwise pass BIDS validation. ezBIDS is agnostic with regard to how users respond to these warnings, meaning that users can ignore warnings and proceed if they so choose, since warnings do not preclude BIDS compliance.
+
 !!! info ezBIDS and dcm2niix
     ezBIDS, like most BIDS converters, uses [dcm2niix](https://github.com/rordenlab/dcm2niix) to convert DICOM files to NIfTI, JSON, .bval, and .bvec files. The set of *dcm2niix* output files is required by BIDS. If dcm2niix generates an error for a specific series of DICOMS during the conversion process, ezBIDS will display the message for users.
 
@@ -167,5 +175,3 @@ Once a BIDS-compliant dataset is generated, users can click on the blue "Downloa
     | _Are there any differences in how ezBIDS stores users data for example when downloading the BIDS data or pushing the data to OpenNeuro.org, brainlife.io?_ | No, all data sets are treated the same, software services process the data without human intervention and regardless of user selections. |
     | _If users’ data were collected under an IRB that states that the data will only be stored on university servers; will I be non-compliant if I use ezBIDS on these data?_ | The answer is “possibly, yes,” and it is such only if the IRB does not specify what it is meant by the phrase “to store data,” i.e., long term preservation. ezBIDS is not a long-term preservation system nor a data archive. ezBIDS stores users data, in most cases, outside of the users’ University servers for up to 5 days for the sole purpose to provide a service to the user and without human intervention or actions on the data. |
     | _Will my IRB consider this to be data sharing, given that the data are temporarily being stored on non-university servers?_ | Generally data sharing is between two humans or human groups. ezBIDS is a software service and no human receives, accesses or operates on the data, so technically the data is never shared. Yet, different IRBs make different decisions on this issue, and it will be important for the user to discuss this with their IRB prior to using ezBIDS, if the user believes concerns might arise from using the service. The ezBIDS team provides boilerplate text to assist the user in these discussions. 
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