aramis-lab · AliceJoubert · Sep 11, 2024 · Sep 10, 2024 · Sep 10, 2024 · Sep 10, 2024
diff --git a/docs/CAPS/Introduction.md b/docs/CAPS/Introduction.md
@@ -121,12 +121,12 @@ groups/
 
 ### Subject level example with longitudinal analysis
 
-This CAPS folder contains the outputs of longitudinal segmentations performed with [FreeSurfer](../Third-party.md#freesurfer) for a fictional participant `CLNC01` at sessions `M000` and `M018`.
+This CAPS folder contains the outputs of longitudinal segmentations performed with [FreeSurfer](../Software/Third-party.md#freesurfer) for a fictional participant `CLNC01` at sessions `M000` and `M018`.
 First, the [`t1-freesurfer` pipeline](../Pipelines/T1_FreeSurfer.md) is run on the two sessions.
 Then, the [`t1-freesurfer-longitudinal` pipeline](../Pipelines/T1_FreeSurfer_Longitudinal.md) will compute the intra-subject template `sub-CLNC01_long-M000M018` using the `M000` and `M018` sessions.
 This template is finally used to longitudinally correct the segmentations, whose results are stored in the `sub-CLNC01_ses-M000.long.sub-CLNC01_long-M000M018` and `sub-CLNC01_ses-M018.long.sub-CLNC01_long-M000M018` folders.
 
-Of note, the `<time_point_id>.long.<template_id>` naming comes from [FreeSurfer](../Third-party.md#freesurfer) when running the longitudinal `recon-all` command.
+Of note, the `<time_point_id>.long.<template_id>` naming comes from [FreeSurfer](../Software/Third-party.md#freesurfer) when running the longitudinal `recon-all` command.
 
 ```Text
 dataset_description.json

diff --git a/docs/CAPS/Specifications.md b/docs/CAPS/Specifications.md
@@ -135,9 +135,9 @@ subjects/
                   └─ <source_file>_segm-<segm>_dartelinput.nii.gz
 ```
 
-- The `modulated-{on|off}` key indicates if modulation has been used in [SPM](../Third-party.md#spm12) to compensate for the effect of spatial normalization.
+- The `modulated-{on|off}` key indicates if modulation has been used in [SPM](../Software/Third-party.md#spm12) to compensate for the effect of spatial normalization.
 - The possible values for the `segm-<segm>` key/value are: `graymatter`, `whitematter`, `csf`, `bone`, `softtissue`, and `background`.
-- The T1 image in `Ixi549Space` (reference space of the TPM) is obtained by applying the transformation obtained from the [SPM](../Third-party.md#spm12) segmentation routine to the T1 image in native space.
+- The T1 image in `Ixi549Space` (reference space of the TPM) is obtained by applying the transformation obtained from the [SPM](../Software/Third-party.md#spm12) segmentation routine to the T1 image in native space.
 
 #### DARTEL
 
@@ -152,7 +152,7 @@ groups/
 ```
 
 - The final group template is `<group_id>_template.nii.gz`.
-- The `<group_id>_iteration-<index>_template.nii.gz` obtained at each iteration will only be used when obtaining flow fields for registering a new image into an existing template ([SPM](../Third-party.md#spm12) DARTEL existing templates procedure).
+- The `<group_id>_iteration-<index>_template.nii.gz` obtained at each iteration will only be used when obtaining flow fields for registering a new image into an existing template ([SPM](../Software/Third-party.md#spm12) DARTEL existing templates procedure).
 
 !!! Note "Note for SPM experts"
     The original name of `<group_id>_iteration-<index>_template.nii.gz` is `Template<index>.nii`.
@@ -191,7 +191,7 @@ Statistics files (with `_statistics.tsv` suffix) are detailed in [appendix](#app
 
 ### `t1-freesurfer` - FreeSurfer-based processing of T1-weighted MR images
 
-The outputs of the `t1-freesurfer` pipeline are split into two sub-folders, the first one containing the [FreeSurfer](../Third-party.md#freesurfer) outputs and a second with additional outputs specific to Clinica.
+The outputs of the `t1-freesurfer` pipeline are split into two sub-folders, the first one containing the [FreeSurfer](../Software/Third-party.md#freesurfer) outputs and a second with additional outputs specific to Clinica.
 
 FreeSurfer outputs:
 
@@ -285,7 +285,7 @@ subjects/
 
 ### FreeSurfer longitudinal outputs
 
-The outputs are split into two sub-folders, the first containing the [FreeSurfer](../Third-party.md#freesurfer) longitudinal outputs and a second with additional outputs specific to Clinica.
+The outputs are split into two sub-folders, the first containing the [FreeSurfer](../Software/Third-party.md#freesurfer) longitudinal outputs and a second with additional outputs specific to Clinica.
 
 ```Text
 dataset_description.json

diff --git a/docs/Converters/ADNI2BIDS.md b/docs/Converters/ADNI2BIDS.md
@@ -18,7 +18,7 @@
 
 ## Dependencies
 
-If you only [installed the core of Clinica](../Installation.md), this pipeline needs the installation of the [**dcm2niix**](../Third-party.md#dcm2nix) DICOM to NIfTI converter.
+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.
 
 ## Downloading ADNI
 

diff --git a/docs/Converters/AIBL2BIDS.md b/docs/Converters/AIBL2BIDS.md
@@ -21,7 +21,7 @@
 
 ## Dependencies
 
-If you only [installed the core of Clinica](../Installation.md), this pipeline needs the installation of the [**dcm2niix**](../Third-party.md#dcm2nix) DICOM to NIfTI converter.
+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.
 
 ### Downloading AIBL
 

diff --git a/docs/Converters/GENFItoBIDS.md b/docs/Converters/GENFItoBIDS.md
@@ -6,7 +6,7 @@
 
 ## Dependencies
 
-If you only [installed the core of Clinica](../Installation.md), this pipeline needs the installation of the [**dcm2niix**](../Third-party.md#dcm2nix) DICOM to NIfTI converter.
+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.
 
 ## Supported modalities
 

diff --git a/docs/Converters/IXItoBIDS.md b/docs/Converters/IXItoBIDS.md
@@ -21,7 +21,7 @@ DTI ; T1 ; T2 ; PD ; angiography.
 
 
 ### Dependencies
-If you [installed clinica](../Installation.md#install-clinica), this converter needs no further dependencies.
+If you [installed clinica](../Software/Installation.md#install-clinica), this converter needs no further dependencies.
 
 ### Understanding the command line
 ```{ .bash .copy }

diff --git a/docs/Converters/NIFD2BIDS.md b/docs/Converters/NIFD2BIDS.md
@@ -7,7 +7,7 @@
 
 ## Dependencies
 
-If you only [installed the core of Clinica](../Installation.md), this pipeline needs the installation of the [**dcm2niix**](../Third-party.md#dcm2nix) DICOM to NIfTI converter.
+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.
 
 ## Downloading NIFD
 

diff --git a/docs/Converters/UKBtoBIDS.md b/docs/Converters/UKBtoBIDS.md
@@ -19,7 +19,7 @@ The UKB to BIDS converter assumes that the user has already got access to the da
 ## Using the converter
 ### Dependencies
 
-If you [installed the core of Clinica](../Installation.md#install-clinica), this converter needs the [dcm2niix](../Third-party.md#converters) package.
+If you [installed the core of Clinica](../Software/Installation.md#install-clinica), this converter needs the [dcm2niix](../Software/Third-party.md#converters) package.
 
 ### Supported modalities
 

diff --git a/docs/Pipelines/DWI_Connectome.md b/docs/Pipelines/DWI_Connectome.md
@@ -10,7 +10,7 @@ You need to [preprocess your DWI data](./DWI_Preprocessing.md) and run the [`t1-
 
 ## Dependencies
 
-If you only installed the core of Clinica, this pipeline needs the installation of [FSL 6.0](../Third-party.md#fsl), [MRtrix3](../Third-party.md#mrtrix3), and [Freesurfer](../Third-party.md#freesurfer) on your computer.
+If you only installed the core of Clinica, this pipeline needs the installation of [FSL 6.0](../Software/Third-party.md#fsl), [MRtrix3](../Software/Third-party.md#mrtrix3), and [Freesurfer](../Software/Third-party.md#freesurfer) on your computer.
 
 ## Running the pipeline
 
@@ -52,7 +52,7 @@ The main output files are:
     It was built on anatomical MRI of 24 healthy subjects from which 74 cortical ROIs were manually identified in each of the individual hemispheres.
 
 The matrices are encoded as [TSV](../glossary.md#tsv) files without labels for rows and columns.
-These labels are generated by [MRtrix3](../Third-party.md#mrtrix3) and the lookup tables should have been automatically downloaded by Clinica when the `dwi-connectome` pipeline has been run.
+These labels are generated by [MRtrix3](../Software/Third-party.md#mrtrix3) and the lookup tables should have been automatically downloaded by Clinica when the `dwi-connectome` pipeline has been run.
 More precisely, there are two lookup tables for extracting the relevant grey matter parcellations:
 
 - one to extract them from the default FreeSurfer segmentation (desikan_killiany), which should be in `<your_clinica_folder>/clinica/resources/mappings/fs_default.txt`

diff --git a/docs/Pipelines/DWI_DTI.md b/docs/Pipelines/DWI_DTI.md
@@ -12,7 +12,7 @@ To that aim, it mainly relies on the **MRtrix3** [[Tournier et al., 2019](https:
 You need [preprocessed DWI data](../DWI_Preprocessing) prior to running any of these pipelines.
 
 ## Dependencies
-If you only installed the core of Clinica, this pipeline needs the installation of [ANTs v2.5.0](../Third-party.md#ants), [FSL 6.0](../Third-party.md#fsl), and [MRtrix3](../Third-party.md#mrtrix3) on your computer.
+If you only installed the core of Clinica, this pipeline needs the installation of [ANTs v2.5.0](../Software/Third-party.md#ants), [FSL 6.0](../Software/Third-party.md#fsl), and [MRtrix3](../Software/Third-party.md#mrtrix3) on your computer.
 
 ## Running the pipeline
 

diff --git a/docs/Pipelines/DWI_Preprocessing.md b/docs/Pipelines/DWI_Preprocessing.md
@@ -22,9 +22,9 @@ computing a single multiplicative bias field from the corrected b0 image(s) as i
 
 ## Dependencies
 
-If you only installed the core of Clinica, the `dwi-preprocessing-*` pipeline needs the installation of [ANTs](../Third-party.md#ants), [FSL](../Third-party.md#fsl), and [MRtrix3](../Third-party.md#mrtrix3) on your computer.
+If you only installed the core of Clinica, the `dwi-preprocessing-*` pipeline needs the installation of [ANTs](../Software/Third-party.md#ants), [FSL](../Software/Third-party.md#fsl), and [MRtrix3](../Software/Third-party.md#mrtrix3) on your computer.
 
-Extra installation of [Convert3D](../Third-party.md#convert3d) will be needed for the `dwi-preprocessing-using-t1` pipeline.
+Extra installation of [Convert3D](../Software/Third-party.md#convert3d) will be needed for the `dwi-preprocessing-using-t1` pipeline.
 
 ## Running the pipeline
 

diff --git a/docs/Pipelines/FLAIR_Linear.md b/docs/Pipelines/FLAIR_Linear.md
@@ -10,11 +10,11 @@ These steps include:
 
 ## Dependencies
 
-If you only installed the core of Clinica, this pipeline needs the installation of [ANTs](../Third-party.md#ants) on your computer.
+If you only installed the core of Clinica, this pipeline needs the installation of [ANTs](../Software/Third-party.md#ants) on your computer.
 
 !!! tip
     Since clinica `0.9.0` you have the option to rely on [ANTsPy](https://antspyx.readthedocs.io/en/latest/index.html)
-    instead of [ANTs](../Third-party.md#ants) to run this pipeline, which means that the installation of ANTs is not
+    instead of [ANTs](../Software/Third-party.md#ants) to run this pipeline, which means that the installation of ANTs is not
     required in this case. The ANTsPy package is installed with other Python dependencies of Clinica.
     To use this options, you simply need to add the `--use-antspy` option flag to the command line (see below).
     Note however that this is a new and not extensively tested option such that bugs or unexpected
@@ -36,10 +36,10 @@ where:
 On default, cropped images (matrix size 169×208×179, 1 mm isotropic voxels) are generated to reduce the computing power required when training deep learning models.
 Use the option `--uncropped_image` if you do not want to crop the image.
 
-Finally, it is possible to use [ANTsPy](https://antspyx.readthedocs.io/en/latest/index.html) instead of [ANTs](../Third-party.md#ants) by passing the `--use-antspy` flag.
+Finally, it is possible to use [ANTsPy](https://antspyx.readthedocs.io/en/latest/index.html) instead of [ANTs](../Software/Third-party.md#ants) by passing the `--use-antspy` flag.
 
 !!! note
-    The arguments common to all Clinica pipelines are described in [Interacting with clinica](../InteractingWithClinica.md).
+    The arguments common to all Clinica pipelines are described in [Interacting with clinica](../Software/InteractingWithClinica.md).
 
 !!! tip
     Do not hesitate to type `clinica run flair-linear --help` to see the full list of parameters.

diff --git a/docs/Pipelines/PET_Linear.md b/docs/Pipelines/PET_Linear.md
@@ -24,7 +24,7 @@ You need to have performed the [`t1-linear`](../T1_Linear) pipeline on your T1-w
 
 ## Dependencies
 
-If you only installed the core of Clinica, this pipeline needs the installation of [ANTs](../Third-party.md#ants) on your computer.
+If you only installed the core of Clinica, this pipeline needs the installation of [ANTs](../Software/Third-party.md#ants) on your computer.
 
 ## Running the pipeline
 

diff --git a/docs/Pipelines/PET_Surface.md b/docs/Pipelines/PET_Surface.md
@@ -23,9 +23,9 @@ You need to have performed the [`t1-freesurfer`](../T1_FreeSurfer) pipeline on y
 
 ## Dependencies
 
-If you only installed the core of Clinica, this pipeline needs the installation of [FreeSurfer 6.0](../Third-party.md#freesurfer), [FSL 6.0](../Third-party.md#fsl), and [PETPVC 1.2.4](../Third-party.md#petpvc) (which depends on [ITK 4](../Third-party.md#itk)) on your computer.
+If you only installed the core of Clinica, this pipeline needs the installation of [FreeSurfer 6.0](../Software/Third-party.md#freesurfer), [FSL 6.0](../Software/Third-party.md#fsl), and [PETPVC 1.2.4](../Software/Third-party.md#petpvc) (which depends on [ITK 4](../Software/Third-party.md#itk)) on your computer.
 
-In addition, you also need to either install [SPM12](../Third-party.md#spm12) and [Matlab](../Third-party.md#matlab), or [spm standalone](../Third-party.md#spm12-standalone).
+In addition, you also need to either install [SPM12](../Software/Third-party.md#spm12) and [Matlab](../Software/Third-party.md#matlab), or [spm standalone](../Software/Third-party.md#spm12-standalone).
 
 ## Running the pipeline
 

diff --git a/docs/Pipelines/PET_Surface_Longitudinal.md b/docs/Pipelines/PET_Surface_Longitudinal.md
@@ -27,9 +27,9 @@ You need to have performed the [`t1-freesurfer-longitudinal`](../T1_FreeSurfer_L
 
 ## Dependencies
 
-If you only installed the core of Clinica, this pipeline needs the installation of [FreeSurfer 6.0](../Third-party.md#freesurfer), [FSL 6.0](../Third-party.md#fsl), and [PETPVC 1.2.4](../Third-party.md#petpvc) (which depends on [ITK 4](../Third-party.md#itk)) on your computer.
+If you only installed the core of Clinica, this pipeline needs the installation of [FreeSurfer 6.0](../Software/Third-party.md#freesurfer), [FSL 6.0](../Software/Third-party.md#fsl), and [PETPVC 1.2.4](../Software/Third-party.md#petpvc) (which depends on [ITK 4](../Software/Third-party.md#itk)) on your computer.
 
-In addition, you also need to either install [SPM12](../Third-party.md#spm12) and [Matlab](../Third-party.md#matlab), or [spm standalone](../Third-party.md#spm12-standalone).
+In addition, you also need to either install [SPM12](../Software/Third-party.md#spm12) and [Matlab](../Software/Third-party.md#matlab), or [spm standalone](../Software/Third-party.md#spm12-standalone).
 
 
 ## Running the pipeline

diff --git a/docs/Pipelines/PET_Volume.md b/docs/Pipelines/PET_Volume.md
@@ -20,9 +20,9 @@ You need to have performed the [`t1-volume`](../T1_Volume) pipeline on your T1-w
 
 ## Dependencies
 
-If you only installed the core of Clinica, this pipeline needs the installation of either [SPM12](../Third-party.md#spm12) and [Matlab](../Third-party.md#matlab), or [spm standalone](../Third-party.md#spm12-standalone).
+If you only installed the core of Clinica, this pipeline needs the installation of either [SPM12](../Software/Third-party.md#spm12) and [Matlab](../Software/Third-party.md#matlab), or [spm standalone](../Software/Third-party.md#spm12-standalone).
 
-In addition, if you want to apply partial volume correction (PVC) on your PET data, you will need to install [PETPVC 1.2.4](../Third-party.md#petpvc), which depends on [ITK 4](../Third-party.md#itk).
+In addition, if you want to apply partial volume correction (PVC) on your PET data, you will need to install [PETPVC 1.2.4](../Software/Third-party.md#petpvc), which depends on [ITK 4](../Software/Third-party.md#itk).
 
 ## Running the pipeline
 

diff --git a/docs/Pipelines/Stats_Surface.md b/docs/Pipelines/Stats_Surface.md
@@ -28,7 +28,7 @@ Do not hesitate to have a look at the paragraph **[Specifying what surface data
 
 ## Dependencies
 
-If you only installed the core of Clinica, this pipeline needs the installation of [FreeSurfer](../Third-party.md#freesurfer) on your computer.
+If you only installed the core of Clinica, this pipeline needs the installation of [FreeSurfer](../Software/Third-party.md#freesurfer) on your computer.
 
 ## Running the pipeline
 

diff --git a/docs/Pipelines/Stats_Volume.md b/docs/Pipelines/Stats_Volume.md
@@ -9,7 +9,7 @@ Currently, this pipeline mainly handles gray matter maps obtained from T1-weight
 
 ## Dependencies
 
-If you only installed the core of Clinica, this pipeline needs the installation of [Matlab](../Third-party.md#matlab) and [SPM12](../Third-party.md#spm12), or of [SPM standalone](../Third-party.md#spm12-standalone), on your computer.
+If you only installed the core of Clinica, this pipeline needs the installation of [Matlab](../Software/Third-party.md#matlab) and [SPM12](../Software/Third-party.md#spm12), or of [SPM standalone](../Software/Third-party.md#spm12-standalone), on your computer.
 
 ## Running the pipeline
 

diff --git a/docs/Pipelines/T1_FreeSurfer.md b/docs/Pipelines/T1_FreeSurfer.md
@@ -6,7 +6,7 @@ Additionally, from the FreeSurfer outputs, we generate TSV files containing a su
 
 ## Dependencies
 
-If you only installed the core of Clinica, this pipeline needs the installation of [FreeSurfer 6.0](../Third-party.md#freesurfer) on your computer.
+If you only installed the core of Clinica, this pipeline needs the installation of [FreeSurfer 6.0](../Software/Third-party.md#freesurfer) on your computer.
 
 ## Running the pipeline
 

diff --git a/docs/Pipelines/T1_FreeSurfer_Longitudinal.md b/docs/Pipelines/T1_FreeSurfer_Longitudinal.md
@@ -23,7 +23,7 @@ The pipeline requires a prior run of the cross-sectional [`t1-freesurfer`](../T1
 
 ## Dependencies
 
-If you only installed the core of Clinica, this pipeline needs the installation of [FreeSurfer 6.0](../Third-party.md#freesurfer) on your computer.
+If you only installed the core of Clinica, this pipeline needs the installation of [FreeSurfer 6.0](../Software/Third-party.md#freesurfer) on your computer.
 
 ## Running the pipeline