From 138aa843ab26e151876e8c978d03fed4f07258f6 Mon Sep 17 00:00:00 2001 From: Christian Haselgrove Date: Wed, 27 Nov 2024 10:54:06 -0500 Subject: [PATCH 1/5] Add introduction and link to reproinventory to tools --- content/resources/tools/_index.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/content/resources/tools/_index.md b/content/resources/tools/_index.md index 3682409..a31e044 100644 --- a/content/resources/tools/_index.md +++ b/content/resources/tools/_index.md @@ -4,6 +4,8 @@ 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). From 76ff1beecc7e7508a895fd6bdf2dfdf8f9bf447a Mon Sep 17 00:00:00 2001 From: Christian Haselgrove Date: Wed, 27 Nov 2024 11:01:39 -0500 Subject: [PATCH 2/5] Add ReproLake --- content/resources/tools/_index.md | 1 + content/resources/tools/reprolake/_index.md | 23 +++++++++++++++++++++ 2 files changed, 24 insertions(+) create mode 100644 content/resources/tools/reprolake/_index.md diff --git a/content/resources/tools/_index.md b/content/resources/tools/_index.md index a31e044..d103bb5 100644 --- a/content/resources/tools/_index.md +++ b/content/resources/tools/_index.md @@ -13,6 +13,7 @@ This section describes core tools and standards produced by ReproNim. For a mor - [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. +- [ReproLake](reprolake/index.html): Distribution and version control system for all digital objects of science. ## ReproNim Core Standards diff --git a/content/resources/tools/reprolake/_index.md b/content/resources/tools/reprolake/_index.md new file mode 100644 index 0000000..1a74b30 --- /dev/null +++ b/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 From 2f87ac29a7edea82a2bb1aabcb99a48d73b5c82f Mon Sep 17 00:00:00 2001 From: Christian Haselgrove Date: Wed, 27 Nov 2024 11:04:54 -0500 Subject: [PATCH 3/5] Split heudiconv and reproin --- content/resources/tools/_index.md | 3 +- content/resources/tools/heudiconv/_index.md | 35 +++++++++++++++++++++ content/resources/tools/reproin/_index.md | 24 +++----------- 3 files changed, 42 insertions(+), 20 deletions(-) create mode 100644 content/resources/tools/heudiconv/_index.md diff --git a/content/resources/tools/_index.md b/content/resources/tools/_index.md index d103bb5..f552932 100644 --- a/content/resources/tools/_index.md +++ b/content/resources/tools/_index.md @@ -8,7 +8,7 @@ This section describes core tools and standards produced by ReproNim. For a mor ## ReproNim Core Tools -- [Heudiconv/ReproIn](reproin/index.html): Converter from DICOM into structured directory layouts (e.g. BIDS). +- [Heudiconv](heudiconv/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. @@ -20,3 +20,4 @@ This section describes core tools and standards produced by ReproNim. For a mor - [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. +- [ReproIn](reproin/index.html) diff --git a/content/resources/tools/heudiconv/_index.md b/content/resources/tools/heudiconv/_index.md new file mode 100644 index 0000000..a72e65b --- /dev/null +++ b/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 diff --git a/content/resources/tools/reproin/_index.md b/content/resources/tools/reproin/_index.md index b7661cc..84c6c97 100644 --- a/content/resources/tools/reproin/_index.md +++ b/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 From a474eae8ca41380fa8ce32e8e9e6981c75ad37db Mon Sep 17 00:00:00 2001 From: Christian Haselgrove Date: Wed, 27 Nov 2024 11:15:36 -0500 Subject: [PATCH 4/5] Add Nipoppy page --- content/resources/tools/_index.md | 2 +- content/resources/tools/nipoppy/_index.md | 23 +++++++++++++++++++++++ 2 files changed, 24 insertions(+), 1 deletion(-) create mode 100644 content/resources/tools/nipoppy/_index.md diff --git a/content/resources/tools/_index.md b/content/resources/tools/_index.md index f552932..ff4b877 100644 --- a/content/resources/tools/_index.md +++ b/content/resources/tools/_index.md @@ -19,5 +19,5 @@ This section describes core tools and standards produced by ReproNim. For a mor - [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. +- [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) diff --git a/content/resources/tools/nipoppy/_index.md b/content/resources/tools/nipoppy/_index.md new file mode 100644 index 0000000..62a3c29 --- /dev/null +++ b/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 From f616a59f2f8dc8535ad8bf357a424ddfe478247e Mon Sep 17 00:00:00 2001 From: Christian Haselgrove Date: Wed, 27 Nov 2024 11:16:35 -0500 Subject: [PATCH 5/5] Alphabetize tools --- content/resources/tools/_index.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/content/resources/tools/_index.md b/content/resources/tools/_index.md index ff4b877..6395ea2 100644 --- a/content/resources/tools/_index.md +++ b/content/resources/tools/_index.md @@ -8,16 +8,16 @@ This section describes core tools and standards produced by ReproNim. For a mor ## ReproNim Core Tools -- [Heudiconv](heudiconv/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) +- [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)