[DOC] Adding Support page (#1297)

* first proposition * As snippet * Add contributing * Change arch * Put contributing.md back in place + try fix links * Try linking outside docs * Test hooks * Remove hooks * 2e test hooks * Test more with hook * Test hooks on startup * Remove hooks * Test link with html * Test with html * Test fix broken links from Third Party * Test fix link third party * Test fix link third party2 * Apply to all links * Test link on Home * Add home folder * Test contributing.md kinking * Test snippet for contributing * Add symlink * Fix symlink * Remove .md from nav * Changes upon suggestions * Last fix * Fix lasts links
aramis-lab · Sep 25, 2024 · 393e4c4 · 393e4c4
1 parent 05c3e69
commit 393e4c4
Show file tree

Hide file tree

Showing 12 changed files with 62 additions and 54 deletions.
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,4 +1,4 @@
-# Contributing to this repo
+# Contributing to Clinica
 
 There are many ways in which you can contribute to the ongoing development of
 this project. For example, you can:

diff --git a/docs/Converters/ADNI2BIDS.md b/docs/Converters/ADNI2BIDS.md
@@ -1,7 +1,7 @@
 <!-- markdownlint-disable MD007 MD046 -->
 # `adni-to-bids` – Conversion of the Alzheimer’s Disease Neuroimaging Initiative (ADNI) to BIDS
 
-!!! quote "Description adapted from the [ADNI website](http://adni.loni.usc.edu)"
+??? quote "Description adapted from the [ADNI website](http://adni.loni.usc.edu)"
     ADNI is a global research effort that actively supports the investigation and development of treatments that slow or stop the progression of Alzheimer's disease (AD).
     This multisite, longitudinal study assesses clinical, imaging, genetic and biospecimen biomarkers through the process of normal aging to mild cognitive impairment (MCI) and AD dementia.
     With established, standardized methods for imaging and biomarker collection and analysis, ADNI facilitates a way for scientists to conduct cohesive research and share compatible data with other researchers around the world.
@@ -16,6 +16,9 @@
     | Duration / Start date   | 5 years / October 2004 | 2 years / September 2009 | 5 years / September 2011 | 5 years / September 2016 |
     | Cohort                  | 200 elderly controls + 400 MCI + 200 AD | Existing ADNI-1 + 200 early MCI | Existing ADNI-1 and ADNI-GO + 150 elderly controls + 100 early MCI + 150 late MCI + 150 AD | Existing ADNI-1, ADNI-GO, ADNI-2 + 133 elderly controls + 151 MCI + 87 AD |
 
+!!! warning "Supported ADNI versions"
+    Clinica is currently able to convert ADNI 1, GO, 2 and 3. It is not ready for ADNI 4.
+
 ## Dependencies
 
 If you only [installed the core of Clinica](../Software/Installation.md), this pipeline needs the installation of the [**dcm2niix**](../Software/Third-party.md#dcm2nix) DICOM to NIfTI converter.

diff --git a/docs/index.md → docs/Home/index.md b/docs/index.md → docs/Home/index.md
@@ -3,17 +3,18 @@
 
 ## What is Clinica ?
 Clinica is a software platform for clinical neuroscience research studies using multimodal data and most often longitudinal follow-up.
-You can learn more on [this page](WhatIsClinica).
+You can learn more on [this page](../WhatIsClinica.md).
 
 ## Installation
 
 Clinica can be installed on **MacOS** and **Linux** (CentOS or Debian/Ubuntu) machines,
 and possibly on Windows computers with a Linux Virtual Machine.
 We assume that users installing and using Clinica are comfortable using the command line.
 
-- [Installation](Software/Installation.md)
-- [Third-party software](Software/Third-party.md)  
-- [Interacting with Clinica](Software/InteractingWithClinica.md)
+- [Installation](../Software/Installation.md)
+- [Third-party software](../Software/Third-party.md)  
+- [Interacting with Clinica](../Software/InteractingWithClinica.md)
+- [Contributing to Clinica](../Software/contributing.md)
 
 <!--
 ### Installing Clinica using Docker
@@ -31,8 +32,8 @@ Installation instructions are available [here](./ICMClusterInstallation).
 
 ### Clinica environment
 
-- [BIDS: the input data structure](BIDS)
-- [CAPS: the processed data structure](CAPS/Introduction)
+- [BIDS: the input data structure](../BIDS.md)
+- [CAPS: the processed data structure](../CAPS/Introduction.md)
 
 ### Pipelines (`clinica run`)
 
@@ -50,16 +51,16 @@ Clinica provides tools to curate several publicly available neuroimaging dataset
 
 ### I/O tools (`clinica iotools`)
 
-- [Data handling tools for BIDS and CAPS compliant datasets](IO)
+- [Data handling tools for BIDS and CAPS compliant datasets](../IO)
 
 ### Visualize pipeline outputs (`clinica visualize`)
 
 Clinica allows visualization of the main outputs of some pipelines.
-Currently only supported for the [`t1-freesurfer` pipeline](Pipelines/T1_FreeSurfer).
+Currently only supported for the [`t1-freesurfer` pipeline](../Pipelines/T1_FreeSurfer).
 
 ## Clinica at conferences
 
-Find on [this page](ClinicaConferences) the presentations and demo materials used when we showcase Clinica.
+Find on [this page](../ClinicaConferences) the presentations and demo materials used when we showcase Clinica.
 
 ## Support
 
@@ -86,4 +87,4 @@ Each page includes text to cite the software packages that are used by Clinica
 
 ---
 
-![Clinica_Partners_Banner](img/Clinica_Partners_Banner.png)
+![Clinica_Partners_Banner](../img/Clinica_Partners_Banner.png)
diff --git a/docs/Software/Installation.md b/docs/Software/Installation.md
@@ -3,8 +3,6 @@
 
 You will find below the steps for installing Clinica on **Linux** or **Mac**.
 
-Please do not hesitate to contact us on the [forum](https://groups.google.com/forum/#!forum/clinica-user) or [GitHub](https://github.com/aramis-lab/clinica/issues) if you encounter any issues.
-
 ## Prepare your Python environment with miniconda
 
 You will need a Python environment to run Clinica.

diff --git a/docs/Software/InteractingWithClinica.md b/docs/Software/InteractingWithClinica.md
@@ -133,9 +133,3 @@ You might also use `CNvsAD`, for instance, as group ID for a statistical group c
 --8<-- "snippets/converters_options.md"
 
 --8<-- "snippets/known_issues.md:matlab"
-
-
-## Support
-
-- You can use the [Clinica Google Group](https://groups.google.com/forum/#!forum/clinica-user) to ask for help!
-- Report an issue on [GitHub](https://github.com/aramis-lab/clinica/issues).
diff --git a/docs/Software/Third-party.md b/docs/Software/Third-party.md
@@ -32,11 +32,11 @@ and will be lost if you re-launch your terminal.
 Some converters require **dcm2niix** to transform DICOM files into NIfTI :
 
 <div class="grid">
-  <a href="./../Converters/ADNI2BIDS/index.html" class="card">adni-to-bids</a>
-  <a href="./../Converters/AIBL2BIDS/index.html" class="card">aibl-to-bids</a>
-  <a href="./../Converters/GENFItoBIDS/index.html" class="card">genfi-to-bids</a>
-  <a href="./../Converters/NIFD2BIDS/index.html" class="card">nifd-to-bids</a>
-  <a href="./../Converters/UKBtoBIDS/index.html" class="card">ukb-to-bids</a>
+  <a href="./../../Converters/ADNI2BIDS/index.html" class="card">adni-to-bids</a>
+  <a href="./../../Converters/AIBL2BIDS/index.html" class="card">aibl-to-bids</a>
+  <a href="./../../Converters/GENFItoBIDS/index.html" class="card">genfi-to-bids</a>
+  <a href="./../../Converters/NIFD2BIDS/index.html" class="card">nifd-to-bids</a>
+  <a href="./../../Converters/UKBtoBIDS/index.html" class="card">ukb-to-bids</a>
 </div>
 
 ### DCM2NIX
@@ -249,6 +249,7 @@ You can find more details about `SPM12` on their [website](http://www.fil.ion.uc
     ??? warning "MacOS Big Sur"
         For systems running on MacOS Big Sur, a [development version of SPM12](https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/) as well as a more recent release of the MCR (minimum 2019a) are required.
 
+Then :
 
 1. Make sure to have the following environment variable defined:
     ```{ .bash .copy }

diff --git a/docs/Software/contributing.md b/docs/Software/contributing.md
@@ -0,0 +1 @@
+../../CONTRIBUTING.md
diff --git a/docs/snippets/abbreviations.md b/docs/snippets/abbreviations.md
@@ -1,4 +1,5 @@
 *[BIDS] : Brain Imaging Data Structure
+*[CAPS] : ClinicA Processed Structure
 *[DTI] : Diffusion Tensor Imaging
 *[DWI] : Diffusion Weighted Imaging
 *[CSV] : Comma-Separated Values

diff --git a/docs/snippets/inventory_converters.md b/docs/snippets/inventory_converters.md
@@ -1,10 +1,10 @@
 
-- `adni-to-bids` - [ADNI: Alzheimer’s Disease Neuroimaging Initiative](../Converters/ADNI2BIDS.md)
-- `aibl-to-bids` - [AIBL: Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageing](../Converters/AIBL2BIDS.md)
-- `genfi-to-bids` - [GENFI:Genetic Frontotemporal dementia Initiative](../Converters/GENFItoBIDS.md)
-- `habs-to-bids` - [HABS: Harvard Aging Brain Study](../Converters/HABS2BIDS.md)
-- `ixi-to-bids` - [IXI: Information eXtraction from Images](../Converters/IXItoBIDS.md)
-- `nifd-to-bids` - [NIFD: Neuroimaging in Frontotemporal Dementia](../Converters/NIFD2BIDS.md)
-- `oasis-to-bids` - [OASIS: Open Access Series of Imaging Studies](../Converters/OASIS2BIDS.md)
-- `oasis3-to-bids` - [OASIS-3: Longitudinal Neuroimaging, Clinical, and Cognitive Dataset for Normal Aging and Alzheimer’s Disease](../Converters/OASIS3TOBIDS.md)
-- `ukb-to-bids` - [UK Biobank: Large-scale biomedical database and research resource in the United Kingdom](../Converters/UKBtoBIDS.md)
+- `adni-to-bids` - [ADNI: Alzheimer’s Disease Neuroimaging Initiative](./../Converters/ADNI2BIDS.md)
+- `aibl-to-bids` - [AIBL: Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageing](./../Converters/AIBL2BIDS.md)
+- `genfi-to-bids` - [GENFI:Genetic Frontotemporal dementia Initiative](./../Converters/GENFItoBIDS.md)
+- `habs-to-bids` - [HABS: Harvard Aging Brain Study](./../Converters/HABS2BIDS.md)
+- `ixi-to-bids` - [IXI: Information eXtraction from Images](./../Converters/IXItoBIDS.md)
+- `nifd-to-bids` - [NIFD: Neuroimaging in Frontotemporal Dementia](./../Converters/NIFD2BIDS.md)
+- `oasis-to-bids` - [OASIS: Open Access Series of Imaging Studies](./../Converters/OASIS2BIDS.md)
+- `oasis3-to-bids` - [OASIS-3: Longitudinal Neuroimaging, Clinical, and Cognitive Dataset for Normal Aging and Alzheimer’s Disease](./../Converters/OASIS3TOBIDS.md)
+- `ukb-to-bids` - [UK Biobank: Large-scale biomedical database and research resource in the United Kingdom](./../Converters/UKBtoBIDS.md)
diff --git a/docs/snippets/inventory_pipelines.md b/docs/snippets/inventory_pipelines.md
@@ -1,29 +1,30 @@
 
 - Anatomical MRI
-    - `t1-linear` - [Linear processing of T1w MR images](../Pipelines/T1_Linear.md): affine registration to the MNI standard space of T1 images
-    - `flair-linear` - [Linear processing of FLAIR images](../Pipelines/FLAIR_Linear.md): affine registration to the MNI standard space of FLAIR images
-    - `t1-volume` - [Processing of T1w MR images using SPM](../Pipelines/T1_Volume.md): tissue segmentation and spatial normalization
-    - `t1-freesurfer` - [Processing of T1w MR images using FreeSurfer](../Pipelines/T1_FreeSurfer.md): cortical surface, subcortical structures and volumetrics
-    - `t1-freesurfer-longitudinal` - [Longitudinal processing of T1w MR images using FreeSurfer](../Pipelines/T1_FreeSurfer_Longitudinal.md): cortical surface, subcortical structures and volumetrics
+    - `t1-linear` - [Linear processing of T1w MR images](./../Pipelines/T1_Linear.md): affine registration to the MNI standard space of T1 images
+    - `flair-linear` - [Linear processing of FLAIR images](./../Pipelines/FLAIR_Linear.md): affine registration to the MNI standard space of FLAIR images
+    - `t1-volume` - [Processing of T1w MR images using SPM](./../Pipelines/T1_Volume.md): tissue segmentation and spatial normalization
+    - `t1-freesurfer` - [Processing of T1w MR images using FreeSurfer](./../Pipelines/T1_FreeSurfer.md): cortical surface, subcortical structures and volumetrics
+    - `t1-freesurfer-longitudinal` - [Longitudinal processing of T1w MR images using FreeSurfer](./../Pipelines/T1_FreeSurfer_Longitudinal.md): cortical surface, subcortical structures and volumetrics
+
 - Diffusion MRI (DWI)
-    - `dwi-preprocessing-*` - [DWI pre-processing](../Pipelines/DWI_Preprocessing.md): correction of head motion, magnetic susceptibility, eddy current and bias field induced distortions
-    - `dwi-dti` - [DTI scalar maps (FA, MD, AD, RD) and spatial normalization](../Pipelines/DWI_DTI.md): extraction of DTI-based measures (FA, MD, AD, RD)
-    - `dwi-connectome` - [Construction of structural connectome](../Pipelines/DWI_Connectome.md): computation of fiber orientation distributions, tractogram and connectome
+    - `dwi-preprocessing-*` - [DWI pre-processing](./../Pipelines/DWI_Preprocessing.md): correction of head motion, magnetic susceptibility, eddy current and bias field induced distortions
+    - `dwi-dti` - [DTI scalar maps (FA, MD, AD, RD) and spatial normalization](./../Pipelines/DWI_DTI.md): extraction of DTI-based measures (FA, MD, AD, RD)
+    - `dwi-connectome` - [Construction of structural connectome](./../Pipelines/DWI_Connectome.md): computation of fiber orientation distributions, tractogram and connectome
 
 - PET
-    - [Introduction to concepts used in the PET pipelines](../Pipelines/PET_Introduction.md): partial volume correction and standardized uptake value ratio (SUVR) map computation
-    - `pet-linear` - [Linear processing of PET images](../Pipelines/PET_Linear.md): affine registration to the MNI standard space and intensity normalization
-    - `pet-volume` - [Volume-based processing of PET images](../Pipelines/PET_Volume.md): registration to T1w MRI, intensity normalization, partial volume correction and spatial normalization
-    - `pet-surface` - [Surface-based processing of PET images](../Pipelines/PET_Surface.md): projection of the PET signal onto the subject’s cortical surface
-    - `pet-surface-longitudinal` - [Surface-based longitudinal processing of PET images](../Pipelines/PET_Surface_Longitudinal.md): projection of the PET signal onto the subject’s cortical surface
+    - [Introduction to concepts used in the PET pipelines](./../Pipelines/PET_Introduction.md): partial volume correction and standardized uptake value ratio (SUVR) map computation
+    - `pet-linear` - [Linear processing of PET images](./../Pipelines/PET_Linear.md): affine registration to the MNI standard space and intensity normalization
+    - `pet-volume` - [Volume-based processing of PET images](./../Pipelines/PET_Volume.md): registration to T1w MRI, intensity normalization, partial volume correction and spatial normalization
+    - `pet-surface` - [Surface-based processing of PET images](./../Pipelines/PET_Surface.md): projection of the PET signal onto the subject’s cortical surface
+    - `pet-surface-longitudinal` - [Surface-based longitudinal processing of PET images](./../Pipelines/PET_Surface_Longitudinal.md): projection of the PET signal onto the subject’s cortical surface
 
 - Statistics
-    - `statistics-surface` - [Surface-based mass-univariate analysis with SurfStat](../Pipelines/Stats_Surface.md)
-    - `statistics-volume` - [Volume-based mass-univariate analysis with SPM](../Pipelines/Stats_Volume.md)
+    - `statistics-surface` - [Surface-based mass-univariate analysis with SurfStat](./../Pipelines/Stats_Surface.md)
+    - `statistics-volume` - [Volume-based mass-univariate analysis with SPM](./../Pipelines/Stats_Volume.md)
 
 - Machine Learning
-    - `machinelearning-prepare-spatial-svm` - [Prepare input data for spatially regularized SVM](../Pipelines/MachineLearning_PrepareSVM.md)
-    - `machinelearning-classification` - [Classification based on machine learning](../Pipelines/MachineLearning_Classification.md)
+    - `machinelearning-prepare-spatial-svm` - [Prepare input data for spatially regularized SVM](./../Pipelines/MachineLearning_PrepareSVM.md)
+    - `machinelearning-classification` - [Classification based on machine learning](./../Pipelines/MachineLearning_Classification.md)
 
 - Deep learning
     - You can use the [ClinicaDL framework](https://clinicadl.readthedocs.io/) for the reproducible processing of neuroimaging data with deep learning methods.
diff --git a/docs/snippets/support.md b/docs/snippets/support.md
@@ -0,0 +1,5 @@
+## Contact us !
+
+- Check for past answers on [Clinica Google Group](https://groups.google.com/forum/#!forum/clinica-user)
+- Start a [discussion](https://github.com/aramis-lab/clinica/discussions) on GitHub
+- Report an [issue](https://github.com/aramis-lab/clinica/issues) on Github
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -13,6 +13,7 @@ repo_url: https://github.com/aramis-lab/clinica
 # Copyright
 copyright: Copyright &copy; 2016-2024 Clinica contributors
 
+
 # Configuration
 theme:
   name: material
@@ -63,11 +64,12 @@ markdown_extensions:
   - md_in_html
   - abbr
   - attr_list
-  - md_in_html
   - pymdownx.snippets:
       base_path: docs
       auto_append:
         - snippets/abbreviations.md
+        - snippets/support.md
+
   - toc:
       permalink: True
   - pymdownx.tabbed:
@@ -78,11 +80,12 @@ not_in_nav: |
 
 # Page tree
 nav:
-  - Home: index.md
+  - Home: Home/index.md
   - Setting-up for Clinica:
     - Installation: Software/Installation.md
     - Third-party software: Software/Third-party.md
     - Interacting with Clinica: Software/InteractingWithClinica.md
+    - Contributing to Clinica : Software/contributing.md
   - Clinica environment:
     - What is Clinica?: WhatIsClinica.md
     - BIDS: BIDS.md
@@ -124,12 +127,12 @@ nav:
     - OASIS-3 to BIDS: Converters/OASIS3TOBIDS.md
     - UK Biobank to BIDS: Converters/UKBtoBIDS.md
   - I/O tools:
-    - describe: IO#describe-Describe-a-BIDS-or-CAPS-dataset
     - create-subjects-visits: IO#create-subjects-visits-generate-the-list-all-subjects-and-visits-of-a-given-dataset
     - check-missing-modalities: IO#check-missing-modalities-check-missing-modalities-for-each-subject
     - check-missing-processing: IO#check-missing-processing-check-missing-processing-in-a-caps-directory
     - merge-tsv: IO#merge-tsv-gather-bids-and-caps-data-into-a-single-tsv-file
     - center-nifti: IO#center-nifti-center-the-nifti-files-of-a-bids-directory
+    - describe: IO#describe-Describe-a-BIDS-or-CAPS-dataset
   - Presentations & demos:
     - NOW 2023: ClinicaConferences#neuro-openscience-workshop-2023
     - NOW 2019: ClinicaConferences#neuro-openscience-workshop-2019