Merge pull request #30 from chaselgrove/tools

Update tools

content/resources/tools/_index.md

@@ -4,16 +4,20 @@ date: 2024-10-28T15:14:39-04:00
 weight: 10
 ---
 
+This section describes core tools and standards produced by ReproNim.  For a more comprehensive catalog of resources related to reproducible neuroimaging, please see the [ReproInventory project](https://github.com/ReproNim/ReproInventory).
+
 ## ReproNim Core Tools
 
-- [Heudiconv/ReproIn](reproin/index.html): Converter from DICOM into structured directory layouts (e.g. BIDS).
-- [ReproSchema](reproschema/index.html): A tool for defining, sharing, and reusing structured research protocols, enabling versioning and interoperability across studies.
-- [Neurodocker](neurodocker/index.html)
-- [Neurobagel](neurobagel/index.html): A set of tools to query and share data (clinical and brain imaging) in a fully distributed way, keeping the local governance.
 - [DataLad](datalad/index.html): Distribution and version control system for all digital objects of science.
+- [HeuDiConv](heudiconv/index.html): Converter from DICOM into structured directory layouts (e.g. BIDS).
+- [Neurobagel](neurobagel/index.html): A set of tools to query and share data (clinical and brain imaging) in a fully distributed way, keeping the local governance.
+- [Neurodocker](neurodocker/index.html)
+- [ReproLake](reprolake/index.html): Distribution and version control system for all digital objects of science.
+- [ReproSchema](reproschema/index.html): A tool for defining, sharing, and reusing structured research protocols, enabling versioning and interoperability across studies.
 
 ## ReproNim Core Standards
 
-- [NIDM](nidm/index.html)
 - [BIDS](bids/index.html)
-- Nipoppy: A protocol and a set of tools to help standardize the processing a study that has neuroimaging data.
+- [NIDM](nidm/index.html)
+- [Nipoppy](nipoppy/index.html): A protocol and a set of tools to help standardize the processing a study that has neuroimaging data.
+- [ReproIn](reproin/index.html)

content/resources/tools/heudiconv/_index.md

@@ -0,0 +1,35 @@
+---
+title: "HeuDiConv"
+date: 2024-11-27T11:03:21-05:00
+---
+
+*Flexible DICOM conversion into structured directory layouts.*
+
+### Citation information
+
+RRID:SCR_017427
+
+### Requisite knowledge to use
+
+HeuDiConv (Heuristic DICOM Converter) enables flexible and efficient conversion of spatially reconstructed neuroimaging data from the DICOM format (quasi-ubiquitous in biomedical image acquisition systems, particularly in clinical settings) to BIDS, as well as other file layouts.
+
+### Requisite technical requirements
+
+- Command line
+- Desired project structure (BIDS)
+- Python
+
+### Conformance statement
+
+- Collecting DICOMs from MRI (not NIfTI, PAR/REC, etc)
+- Python OR Docker OR Singularity OR Debian
+- DataLad (optional)
+
+### Links
+
+- [Home page](https://heudiconv.readthedocs.io/)
+- [Tutorial](https://heudiconv.readthedocs.io/en/latest/tutorials.html)
+- [Installation](https://heudiconv.readthedocs.io/en/latest/installation.html)
+- [Full documentation](https://heudiconv.readthedocs.io/)
+- [How to get help 1](https://github.com/nipy/heudiconv/issues) [How to get help 2](https://neurostars.org/tag/heudiconv)
+- Testimonials

content/resources/tools/nipoppy/_index.md

@@ -0,0 +1,23 @@
+---
+title: "Nipoppy"
+date: 2024-11-27T11:05:23-05:00
+---
+
+*Poppies will put them to sleep.*
+
+### Citation information
+
+### Requisite knowledge to use
+
+### Requisite technical requirements
+
+### Conformance statement
+
+### Links
+
+- Home page
+- Tutorial
+- Installation
+- Full documentation
+- How to get help
+- Testimonials

content/resources/tools/reproin/_index.md

@@ -3,33 +3,19 @@ title: "ReproIn"
 date: 2024-10-28T15:17:51-04:00
 ---
 
-*Flexible DICOM conversion into structured directory layouts.*
-
 ### Citation information
 
-RRID:SCR_017427
-
 ### Requisite knowledge to use
 
-HeuDiConv (Heuristic DICOM Converter) enables flexible and efficient conversion of spatially reconstructed neuroimaging data from the DICOM format (quasi-ubiquitous in biomedical image acquisition systems, particularly in clinical settings) to BIDS, as well as other file layouts.
-
 ### Requisite technical requirements
 
-- Command line
-- Desired project structure (BIDS)
-- Python
-
 ### Conformance statement
 
-- Collecting DICOMs from MRI (not NIfTI, PAR/REC, etc)
-- Python OR Docker OR Singularity OR Debian
-- DataLad (optional)
-
 ### Links
 
-- [Home page](https://heudiconv.readthedocs.io/)
-- [Tutorial](https://heudiconv.readthedocs.io/en/latest/tutorials.html)
-- [Installation](https://heudiconv.readthedocs.io/en/latest/installation.html)
-- [Full documentation](https://heudiconv.readthedocs.io/)
-- [How to get help 1](https://github.com/nipy/heudiconv/issues) [How to get help 2](https://neurostars.org/tag/heudiconv)
+- Home page
+- Tutorial
+- Installation
+- Full documentation
+- How to get help 1
 - Testimonials

content/resources/tools/reprolake/_index.md

@@ -0,0 +1,23 @@
+---
+title: "ReproLake"
+date: 2024-11-27T11:00:02-05:00
+---
+
+*The lake is dry.*
+
+### Citation information
+
+### Requisite knowledge to use
+
+### Requisite technical requirements
+
+### Conformance statement
+
+### Links
+
+- Home page
+- Tutorial
+- Installation
+- Full documentation
+- How to get help
+- Testimonials