diff --git a/content/resources/tools/_index.md b/content/resources/tools/_index.md index 3682409..6395ea2 100644 --- a/content/resources/tools/_index.md +++ b/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) 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/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 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 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