Merge branch 'main' into patch-16

content/resources/getting-started/_index.md

@@ -8,18 +8,19 @@ weight: 2
 ReproNim offers best practices, tools and training to implement reproducible neuroimaging in your lab.  Here is a brief overview of our website:
 
 * **New to reproducible neuroimaging?**
-  * Why reproducible neuroimaging
-  * What is reproducible neuroimaging?
+  * [Why reproducible neuroimaging](https://repronim.netlify.app/about/why/)
+  * [What is reproducible neuroimaging?](/about/why/#what-is-reproducible-neuroimaging)
+  * [ReproNim's principles and supporting actions](/about/in-practice/) for reproducible neuroimaging 
 * **Wondering what ReproNim can do for you?**
-  * Meet our exemplary user personas and the issues they face in running neuroimaging studies
-  * View our introduction to the ReproNim way, step-by-step guides on some steps you can take using ReproNim tools to improve your ability to perform robust and shareable neuroimaging studies
+  * Meet our [exemplary user personas and the issues they face in running neuroimaging studies](/resources/getting-started/#meet-our-user-personas)
+  * View our introduction to the [ReproNim approach](/about/repronim-approach/) and some step-by-step tutorials on how to use ReproNim tools to improve your ability to perform robust and shareable neuroimaging studies
 * **Tools and how-to guide:**
-  * Our ReproGuide provides descriptions of our tools and how to use them
+  * Our [Resource](https://repronim.netlify.app/resources/) section provides a listing of [tools](/resources/tools/) and [tutorials](/resources/tutorials/) on how to use them to support principles of reproducible neuroimaging 
 * **Training:**
   * [On-line training course](https://www.repronim.org/teach.html) on a range of basic and more advanced topics related to reproducible neuroimaging
-  * ReproNim Fellows Program:  Become a ReproNim fellow through our train the trainer program
+  * [ReproNim Fellows Program](/fellowship/):  Become a ReproNim fellow through our train the trainer program
 
-## Meet our users personas
+## Meet our user personas
 
 To introduce you to ReproNim, we have created a set of exemplary user personas that represent some typical users and given them a face (through the magic of AI), a set of skills and interests. We then produced a set of basic use cases that showcased how adopting the principles of neuroimaging and ReproNim tools can help them in their goals.
 
@@ -82,13 +83,13 @@ ReproNim can help Sarah learn more about data and software management and other
   * Principle \= planning
 * Implementing data management basics:  Using ReproNim tools to [convert data to the BIDS standard](/resources/tutorials/dicom-to-bids/) and [create a data dictionary](/resources/tutorials/data-dictionary/)
   * Principle:  Data and metadata management
-  * Foundations:  Standards, Annotation
+  * Actions:  Standards, Annotation
 * Implementing software management basics:  [Using Git to manage workflow/pipeline versions](/resources/tutorials/git/)
   * Principle:  Software management
-  * Foundations:  Versioning
+  * Actions:  Versioning
 * Publishing your work as a “Re-executable paper”( \= text, data, code):  Standards-based data sharing through OpenNeuro
   * Principle:  Publishing re-executable papers
-  * Foundations: Standards, Annotation
+  * Actions: Standards, Annotation
 
 ### Richard
 
@@ -108,7 +109,7 @@ ReproNim can help Richard learn how standards such as BIDS and NIDM can help wit
 
 * Advanced data management: Putting your derived data into BIDS derivatives and creating a semantically-enriched  data dictionary using NIDM, a standard for annotating neuroimaging data
   * Principles:  Data management
-  * Foundations:  Standards, annotation
+  * Actions:  Standards, annotation
 * Working with containers:  Using Neurodocker to containerize computational
   * Principles:  Re-executability
 * Advanced data and software management: [DataLad containers/run \+, YODA principles](/resources/tutorials/repronim-containers/)
@@ -154,13 +155,13 @@ ReproNim is not an end to end platform, but has several tools that can take her
 
 * Planning and data management:  Learn how a data collection and annotation framework for behavioral data to be collected can be set up using [ReproSchema and shared across multiple sites](https://repronim.netlify.app/resources/tutorials/reproschema/).
   * Principles:  planning, data management
-  * Foundations:  standards, annotations
+  * Actions:  standards, annotations
 * Basic software management for distributed data: [Curating and processing a single study to generate standardized, analysis-ready data to participate in distributed projects using Nipoppy](/resources/tutorials/nipoppy/)
   * Principles:  Software management
-  * Standards:  Standards, annotation
+  * Actions:  Standards, annotation
 * Advanced data management:  Adding standards and semantics to data dictionaries to promote data harmonization and findability
   * Principles:  data management, FAIR
-  * Foundations:  Standards, Annotation
+  * Actions:  Standards, Annotation
 * Advanced metadata management: [Searching and sharing metadata through ReproPond and ReproLake](/resources/tutorials/pond-lake/)
   * Principles:  Metadata management
-  * Foundations:  Standards, Annotation
+  * Actions:  Standards, Annotation

content/resources/tools/reproschema/_index.md

@@ -38,6 +38,7 @@ ReproSchema applies reproducible neuroimaging principles to assessments, allowin
 - Tutorials:
   - https://www.repronim.org/reproschema/user-guide/create-new-protocol/
   - https://www.repronim.org/reproschema/tutorials/using-reproschema/
+  - [Set up a data collection and annotation framework for multi-site behavioral studies using ReproSchema](/resources/tutorials/reproschema/)
 - Installation: https://pypi.org/project/reproschema/
 - Full documentation: https://www.repronim.org/reproschema/
 - How to get help: https://github.com/ReproNim/reproschema/issues

content/resources/tutorials/_index.md

@@ -8,4 +8,33 @@ TODO: [GH 124](https://github.com/ReproNim/repronim.org/issues/124)
 
 To get started with ReproNim, we have created a set of  tutorials to show how ReproNim’s tools and services support best practices laid out in [ReproNim’s principles of Reproducible Neuroimaging](/about/in-practice/) and [ReproNim’s 4 Core Actions](/about/in-practice/).  We have organized these tutorials based on our [user personas](/resources/getting-started/) to illustrate how ReproNim’s tools can meet the needs of different types of users with different skill sets and objectives. These tutorials are designed in a modular fashion, showing how individual steps to improve reproducibility can be fit together into an [overall reproducible workflow](/about/repronim-approach/).  
 
-Tutorials are organized into basic and more advanced approaches. Each tutorial is organized in a similar fashion,  providing a list of tools, necessary skills and system requirements, along with step by step instructions to implement and use the tools.    
+Tutorials are organized into basic and more advanced approaches. Each tutorial is organized in a similar fashion,  providing a list of tools, necessary skills and system requirements, along with step by step instructions to implement and use the tools. Below we provide a list of available tutorials, organized according to [ReproNim’s principles of Reproducible Neuroimaging](/about/in-practice/):
+
+**Principle 1:  Study Planning**
+
+* Creating a [neuroimaging data management and sharing plan](/resources/tutorials/data-management-and-sharing/)
+* Set up a data collection and annotation framework for a multisite study using [ReproSchema](https://repronim.netlify.app/resources/tutorials/reproschema/).
+
+**Principle 2: Data and metadata management**
+
+      * Actions: Standards, Annotation and Provenance, Version control 
+
+* *Basic:*  Using ReproNim tools to [convert data to the BIDS standard](/resources/tutorials/dicom-to-bids/) and [create a data dictionary](/resources/tutorials/data-dictionary/)
+* *Basic+:*  Adding standards and semantics to data dictionaries to promote data harmonization and findability
+* *Advanced:* Putting your derived data into BIDS derivatives and creating a semantically-enriched  data dictionary using NIDM, a standard for annotating neuroimaging data
+* *Advanced:* [DataLad containers/run \+, YODA principles](/resources/tutorials/repronim-containers/)
+* *Advanced:* [Searching and sharing metadata through ReproPond and ReproLake](/resources/tutorials/pond-lake/)
+
+**Principle 3: Software management**
+
+      * Actions: Version control, Annotation, Use containers
+
+* *Basic:*  [Using Git to manage workflow/pipeline versions](/resources/tutorials/git/)
+* *Basic+:* [Curating and processing a single study to generate standardized, analysis-ready data to participate in distributed projects using *
+  Nipoppy](/resources/tutorials/nipoppy/)
+* *Basic+:* Working with containers:  Using Neurodocker to containerize computational
+* *Advanced:* [DataLad containers/run \+, YODA principles](/resources/tutorials/repronim-containers/)
+
+**Principle 4:  Publish everything**
+
+* Publishing your work as a “Re-executable paper”( \= text, data, code):  Standards-based data sharing through OpenNeuro

content/resources/tutorials/data-dictionary.md

@@ -1,6 +1,6 @@
 ---
 title: Creating a BIDS Data Dictionary and Adding Semantics to for FAIR
-linkTitle: Data dictionary
+linkTitle: Creating a data dictionary
 type: docs
 weight: 5 
 ---

content/resources/tutorials/dicom-to-bids.md

@@ -1,6 +1,6 @@
 ---
 title: Converting DICOM data to BIDS
-linkTitle: DICOM to BIDS
+linkTitle: Converting DICOM to BIDS
 type: docs
 weight: 5 
 ---

content/resources/tutorials/git.md

@@ -1,6 +1,6 @@
 ---
 title: Using Git to manage workflow/pipeline versions
-linkTitle: Git
+linkTitle: Basic software versioning using Git
 type: docs
 weight: 5
 ---

content/resources/tutorials/nipoppy.md

@@ -1,6 +1,6 @@
 ---
 title: Streamlining Neuroimaging Processing with Nipoppy
-linkTitle: Nipoppy
+linkTitle: Higher order process management
 type: docs
 weight: 5 
 ---

content/resources/tutorials/pond-lake.md

@@ -1,6 +1,6 @@
 ---
 title: Advanced metadata management - Sharing and searching metadata through a ReproPond and the ReproLake
-linkTitle: ReproPond and ReproLake
+linkTitle: Search across studies
 type: docs
 weight: 5
 ---

content/resources/tutorials/repronim-containers.md

@@ -1,5 +1,5 @@
 ---
-title: ReproNim Containers and Yoda
+title: Advanced containerization using DataLad
 type: docs
 weight: 5
 ---

content/resources/tutorials/reproschema.md

@@ -1,23 +1,21 @@
 ---
-title: Set Up a Data Collection and Annotation Framework Using ReproSchema for Multi-Site Behavioral Studies
-linkTitle: ReproSchema
+title: Set Up a Data Collection and Annotation Framework for Multi-Site Behavioral Studies Using ReproSchema 
+linkTitle: Planning a distributed project using ReproSchema
 type: docs
 weight: 5 
 ---
 
 **[Reproducible neuroimaging principles](/about/in-practice/#repronims-principles-of-reproducible-neuroimaging)**
+- Principle 2c:  Data and Metadata management: Annotate data using standard, reproducible procedures
 
 **[Actions](/about/in-practice/#repronims-4-core-actions)**
-
 - Standards
 - Annotation  
 
 **Standards**
-
 - BIDS  
 
 **Tools**
-
 - ReproSchema
 
 ## Challenge