From 9e63d4ee5aec872e07f981038edd1bf438cef719 Mon Sep 17 00:00:00 2001 From: AliceJoubert Date: Tue, 10 Sep 2024 17:29:47 +0200 Subject: [PATCH 1/6] First proposition --- docs/CAPS/Introduction.md | 4 +- docs/CAPS/Specifications.md | 10 +- docs/Converters/ADNI2BIDS.md | 2 +- docs/Converters/AIBL2BIDS.md | 2 +- docs/Converters/GENFItoBIDS.md | 2 +- docs/Converters/IXItoBIDS.md | 2 +- docs/Converters/NIFD2BIDS.md | 2 +- docs/Converters/UKBtoBIDS.md | 2 +- docs/Pipelines/DWI_Connectome.md | 4 +- docs/Pipelines/DWI_DTI.md | 2 +- docs/Pipelines/DWI_Preprocessing.md | 4 +- docs/Pipelines/FLAIR_Linear.md | 8 +- docs/Pipelines/PET_Linear.md | 2 +- docs/Pipelines/PET_Surface.md | 4 +- docs/Pipelines/PET_Surface_Longitudinal.md | 4 +- docs/Pipelines/PET_Volume.md | 4 +- docs/Pipelines/Stats_Surface.md | 2 +- docs/Pipelines/Stats_Volume.md | 2 +- docs/Pipelines/T1_FreeSurfer.md | 2 +- docs/Pipelines/T1_FreeSurfer_Longitudinal.md | 2 +- docs/Pipelines/T1_Linear.md | 10 +- docs/Pipelines/T1_Volume.md | 2 +- docs/{ => Software}/Installation.md | 125 +++++++++--------- docs/{ => Software}/InteractingWithClinica.md | 90 ++++--------- docs/{ => Software}/Third-party.md | 5 +- docs/index.md | 44 +----- mkdocs.yml | 10 +- 27 files changed, 147 insertions(+), 205 deletions(-) rename docs/{ => Software}/Installation.md (52%) rename docs/{ => Software}/InteractingWithClinica.md (58%) rename docs/{ => Software}/Third-party.md (98%) diff --git a/docs/CAPS/Introduction.md b/docs/CAPS/Introduction.md index f68cd159c..4b8bf7d14 100644 --- 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 `.long.` naming comes from [FreeSurfer](../Third-party.md#freesurfer) when running the longitudinal `recon-all` command. +Of note, the `.long.` 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 index aaee9434c..a8b5dee95 100644 --- a/docs/CAPS/Specifications.md +++ b/docs/CAPS/Specifications.md @@ -135,9 +135,9 @@ subjects/ └─ _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-` 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 `_template.nii.gz`. -- The `_iteration-_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 `_iteration-_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 `_iteration-_template.nii.gz` is `Template.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 index c657c9771..26241dda5 100644 --- 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 index 5f48eddcb..72e9dbd2c 100644 --- 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 index c58dacb35..c77648ab6 100644 --- 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 index 2c8b94ce5..6d9ee1a16 100644 --- 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 index 36088045a..fc0d811ee 100644 --- 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 index 66105401a..c04b63582 100644 --- 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 index 6fa4495aa..42b5c620e 100644 --- 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 `/clinica/resources/mappings/fs_default.txt` diff --git a/docs/Pipelines/DWI_DTI.md b/docs/Pipelines/DWI_DTI.md index 2dcc51eea..86290ecfa 100644 --- 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 index 552710d20..d9d951977 100644 --- 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 index 74c404b00..afd0ed3fd 100644 --- 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 index ceea8a334..883508cff 100644 --- 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 index 6c6dada3a..b4e5639e7 100644 --- 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 index f2b74ef47..d11dbe5a9 100644 --- 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 index aeb23d365..55138f949 100644 --- 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 index e4b51d1ca..a5a8c6dd8 100644 --- 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 index 485c7d642..c4aadc352 100644 --- 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 index 27474652f..e056c8840 100644 --- 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 index 6e4211619..2ee45a617 100644 --- 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 diff --git a/docs/Pipelines/T1_Linear.md b/docs/Pipelines/T1_Linear.md index 59da5ac1c..fb53f80d8 100644 --- a/docs/Pipelines/T1_Linear.md +++ b/docs/Pipelines/T1_Linear.md @@ -12,11 +12,11 @@ This pipeline was designed as a prerequisite for the [`extract](https://clinicad ## 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 @@ -39,16 +39,16 @@ On default, cropped images (matrix size 169×208×179, 1 mm isotropic voxels) ar Use the option `--uncropped_image` if you do not want to crop the image. It is also possible to obtain a deterministic result by setting the value of the random seed used by ANTs with the option `--random_seed`. Default will lead to a non-deterministic result. -This option requires [ANTs](../Third-party.md#ants) version `2.3.0` onwards. It is also compatible with [ANTsPy](https://antspyx.readthedocs.io/en/latest/index.html). +This option requires [ANTs](../Software/Third-party.md#ants) version `2.3.0` onwards. It is also compatible with [ANTsPy](https://antspyx.readthedocs.io/en/latest/index.html). It is possible to specify the name of the CAPS dataset that will be created to store the outputs of the pipeline. This works if this CAPS dataset does not exist yet, otherwise the existing name will be kept. This can be achieved with the `--caps-name` option. The provided name will appear in the `dataset_description.json` file, at the root of the CAPS folder (see [CAPS Specifications](../CAPS/Specifications.md#the-dataset_descriptionjson-file) for more details). -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). + [Interacting with clinica](../Software/InteractingWithClinica.md). !!! tip Do not hesitate to type `clinica run t1-linear --help` to see the full list of parameters. diff --git a/docs/Pipelines/T1_Volume.md b/docs/Pipelines/T1_Volume.md index b588f9365..810d2b28c 100644 --- a/docs/Pipelines/T1_Volume.md +++ b/docs/Pipelines/T1_Volume.md @@ -23,7 +23,7 @@ The average gray matter density (also in MNI space) is then computed in each of ## 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) on your computer. +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) on your computer. ## Running the pipeline diff --git a/docs/Installation.md b/docs/Software/Installation.md similarity index 52% rename from docs/Installation.md rename to docs/Software/Installation.md index e605bac1b..f2bf8fd1e 100644 --- a/docs/Installation.md +++ b/docs/Software/Installation.md @@ -1,50 +1,51 @@ -# Installation +# Setting-up for Clinica -You will find below the steps for installing Clinica on Linux or Mac. +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 +## Prepare your Python environment with miniconda You will need a Python environment to run Clinica. We advise you to use [Miniconda](https://docs.conda.io/en/latest/miniconda.html). -Miniconda allows you to install, run, and update Python packages and their dependencies. +It allows you to install, run and update Python packages and their dependencies. It can also create environments to isolate your libraries. To install Miniconda, open a new terminal and type the following commands: -- If you are on Linux: - -```{.sourceCode .bash} -curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o /tmp/miniconda-installer.sh -bash /tmp/miniconda-installer.sh -``` +=== "Linux" + ```{.sourceCode .bash .copy} + curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o /tmp/miniconda-installer.sh + bash /tmp/miniconda-installer.sh + ``` -- If you are on Mac: +=== "MacOS" + ```{.sourceCode .bash .copy} + curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o /tmp/miniconda-installer.sh + bash /tmp/miniconda-installer.sh + ``` -```{.sourceCode .bash} -curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o /tmp/miniconda-installer.sh -bash /tmp/miniconda-installer.sh -``` +!!! danger "Installation path" + Miniconda will ask you where to install it. **Do not forget** to copy the `export PATH` given at the end of the installation. -[Miniconda](https://docs.conda.io/en/latest/miniconda.html) will ask you where to install it. -Do not forget to copy the `export PATH` given at the end of the installation. -If everything went fine, open a new terminal and type `conda info`, it will verify if Conda is installed, check the version and show your Miniconda path. +!!! tip "Verify your miniconda installation" + If everything went fine, open a new terminal and type `conda info`. + It will verify if Conda is installed, check the version and show your Miniconda path. ## Install Clinica The latest release of Clinica can be installed by using the conventional [PyPI package manager](https://pypi.org/project/clinica/) as follows: -```shell +```{.shell .copy} conda create --name clinicaEnv python=3.10 conda activate clinicaEnv pip install clinica ``` -!!! info - Since Clinica `v0.3.5`, Conda installation is no longer available (i.e. +??? warning "Conda installation" + Since Clinica `v0.3.5`, Conda installation **is no longer available** (i.e. `conda create --name clinicaEnv python=3.6 clinica -c Aramislab -c conda-forge` will only install Clinica `v0.3.4`). Pip is now the only way to install the latest version of Clinica. @@ -53,29 +54,30 @@ pip install clinica Depending on the pipeline that you want to use, you need to install **pipeline-specific interfaces**. Not all the dependencies are necessary to run Clinica. -Please refer to [this section](../Third-party) to determine which third-party libraries you need to install. +Please refer to [this section](Third-party.md) to determine which third-party libraries you need to install. ## Shell completion (optional) Shell completion for Clinica is available for [Bash](https://www.gnu.org/software/bash/), [Fish](https://fishshell.com/docs/current/), and [Zsh](https://zsh.sourceforge.io/Doc/). -For Bash, add this to `~/.bashrc`: - -```shell -eval "$(_CLINICA_COMPLETE=source_bash clinica)" -``` - -For Fish, add this to `~/.config/fish/completions/clinica.fish`: - -```shell -eval (env _CLINICA_COMPLETE=source_fish clinica) -``` +=== "Bash" + Add the following to `~/.bashrc`: + ```{.shell .copy} + eval "$(_CLINICA_COMPLETE=source_bash clinica)" + ``` -For Zsh, add this to `~/.zshrc`: +=== "Fish" + Add the following to `~/.config/fish/completions/clinica.fish`: + ```{.shell .copy} + eval (env _CLINICA_COMPLETE=source_fish clinica) + ``` -```shell -eval "$(_CLINICA_COMPLETE=source_zsh clinica)" -``` +=== "Zsh" + Add the following to `~/.zshrc`: + + ```{.shell .copy} + eval "$(_CLINICA_COMPLETE=source_zsh clinica)" + ``` Finally, open a new shell to enable completion. @@ -85,11 +87,11 @@ Finally, open a new shell to enable completion. Now that you have created the Clinica environment, you can activate it: -```{.sourceCode .bash} +```{.sourceCode .bash .copy} conda activate clinicaEnv ``` -!!! success +!!! success "Verify Clinica installation" Congratulations, you have installed Clinica! At this point, you can try the basic `clinica` command and get the following help screen: @@ -111,45 +113,46 @@ conda activate clinicaEnv If you have successfully installed the third-party software packages, you are ready to run any of the pipelines proposed by Clinica. -You can now learn how to [interact with Clinica](../InteractingWithClinica). +You can now learn how to [interact with Clinica](InteractingWithClinica.md). ### Deactivation of the Clinica environment At the end of your session, remember to deactivate your Conda environment: -```{.sourceCode .bash} +```{.sourceCode .bash .copy} conda deactivate ``` -## Developer instructions +## Developer instructions (optional) This section is intended for users who plan to contribute to Clinica or test the current development version. Clinica uses [Poetry](https://python-poetry.org) to manage its development environment. -Please follow these [installation instructions](https://python-poetry.org/docs/#installation) and verify the `poetry` command is correctly setup. -Clone the development branch of Clinica: +1. Please follow these [installation instructions](https://python-poetry.org/docs/#installation) for Poetry and verify the `poetry` command is correctly setup. -```shell -git clone --branch dev https://github.com/aramis-lab/clinica.git -cd clinica -``` +2. Clone the development branch of Clinica: -Create an environment for development: + ```{.shell .copy} + git clone --branch dev https://github.com/aramis-lab/clinica.git + cd clinica + ``` -```shell -conda env create -f environment.yml -``` +3. Create an environment for development: -Install Clinica with the necessary development dependencies: + ```{.shell .copy} + conda env create -f environment.yml + ``` -```shell -conda activate clinica_env -poetry install -``` +4. Install Clinica with the necessary development dependencies: -In case you need to test the documentation locally, install the additional dependencies with: + ```{.shell .copy} + conda activate clinica_env + poetry install + ``` -```shell -poetry install --extras docs -``` +5. In case you need to test the documentation locally, install the additional dependencies with: + + ```{.shell .copy} + poetry install --extras docs + ``` diff --git a/docs/InteractingWithClinica.md b/docs/Software/InteractingWithClinica.md similarity index 58% rename from docs/InteractingWithClinica.md rename to docs/Software/InteractingWithClinica.md index e3d7e1a80..da7c07c1e 100644 --- a/docs/InteractingWithClinica.md +++ b/docs/Software/InteractingWithClinica.md @@ -3,17 +3,16 @@ ## Preparing your data -The easiest way to use Clinica is to have your data organized using the [BIDS standard](http://bids.neuroimaging.io/). +Clinica pipelines require to have your data organized in the [BIDS format](../BIDS.md). BIDS is currently becoming the standard for data organization in the brain imaging community and we strongly recommend to use it. -If your dataset does not follow this standard, you will need to convert it: +If your dataset does not follow this standard, you will need to **convert it** : -If your data are in [DICOM format](https://www.dicomstandard.org), you can use one of the converters referenced on the [BIDS website](https://bids.neuroimaging.io/benefits.html#converters). +- If your data are in [DICOM format](https://www.dicomstandard.org), you can use one of the converters referenced on the [BIDS website](https://bids.neuroimaging.io/benefits.html#converters). +- Otherwise, Clinica includes [converters for public datasets](../index.md#dataset-converters-clinica-convert). -Otherwise, Clinica includes [converters for public datasets](../#dataset-converters-clinica-convert). - -!!! note "Regarding cross-sectional BIDS datasets" - If you run Clinica with a dataset containing no timepoints e.g.: +!!! warning "Clinica and cross-sectional BIDS datasets" + If you run Clinica with a dataset containing **no timepoints** e.g.: ```Text BIDS @@ -25,17 +24,18 @@ Otherwise, Clinica includes [converters for public datasets](../#dataset-convert └── sub-CLNC0001_trc-18FFDG_pet.nii.gz ``` Clinica will propose you to create a new BIDS dataset with a fake timepoint. - This will result to a new dataset resembling to: + This will result in a new dataset resembling to: ```Text BIDS └── sub-CLNC0001 - └── ses-M00 + └── ses-M000 ├── anat │ └── sub-CLNC0001_ses-M000_T1w.nii.gz └── pet ├── sub-CLNC0001_ses-M000_trc-18FFDG_pet.json └── sub-CLNC0001_ses-M000_trc-18FFDG_pet.nii.gz ``` + You should **accept** the creation of this dataset, else Clinica can not run and will fail. !!! tip If you need to create [BIDS](http://bids.neuroimaging.io/) compliant datasets or need tutorials on [BIDS](http://bids.neuroimaging.io/), you can look at this [BIDS Starter Kit](https://github.com/INCF/bids-starter-kit/). @@ -53,39 +53,45 @@ clinica category_of_command command argument options where the arguments are usually your input/output folders, and where the options look like `--flag_1 option_1 --flag_2 option_2`. -!!! note +!!! note "Components order" Please note that the ordering of options on the command-line is not important, whereas arguments must be given in the exact order specified in the documentation (or in the command line helper). ## Categories of command line -The command-line `clinica` has been divided into four main categories. +The command-line `clinica` has been divided into four main categories : ### `clinica run` This category allows the user to run the different image processing and analysis pipelines using the following syntax: ```bash -clinica run modality-pipeline bids_directory caps_directory -tsv my_participants.tsv +clinica run modality-pipeline bids_directory caps_directory options ``` "modality" is a prefix that corresponds to the data modality (e.g. T1, DWI, fMRI, PET) or to the category of processing (machine learning, statistics...). -If you execute `clinica run --help`, you can see the list of `modality-pipeline` available: they correspond to the different pipelines displayed on the [main page of the documentation](..). +If you execute `clinica run --help`, you can see the list of `modality-pipeline` available : + +??? info "Clinica available pipelines" + --8<-- "snippets/inventory_pipelines.md" -!!! note +!!! tip "Clinica run logs" Clinica run logs are written in the current working directory by default. A different directory may be specified by setting the `CLINICA_LOGGING_DIR` environment variable. ### `clinica convert` These tools allow you to convert unorganized datasets from publicly available neuroimaging studies into a [BIDS](http://bids.neuroimaging.io/) hierarchy. -Clinica currently includes some [converters for public datasets](../#dataset-converters-clinica-convert). +Clinica currently includes some converters for public datasets : + +??? info "Clinica available converters" + --8<-- "snippets/inventory_converters.md" ### `clinica iotools` -`iotools` is a set of tools that allows the user to handle [BIDS](http://bids.neuroimaging.io) and [CAPS](../CAPS/Introduction) datasets. +`iotools` is a set of tools that allows the user to handle [BIDS](http://bids.neuroimaging.io) and [CAPS](../CAPS/Introduction.md) datasets. It allows generating lists of subjects or merging all tabular data into a single TSV file for analysis with external statistical software packages. -See [here](../IO) for more details. +See [here](../IO.md) for more details. ### `clinica generate` (for developers) @@ -102,59 +108,21 @@ clinica generate template "Modality My Pipeline" -d output_folder Running a pipeline involves most of the time these two parameters: -- `BIDS_DIRECTORY`, which is the input folder containing the dataset in a [BIDS](../BIDS) hierarchy; -- `CAPS_DIRECTORY`, which is the output folder containing the expected results in a [CAPS](../CAPS/Introduction) hierarchy. -It can be also the input folder containing the dataset in a [CAPS](../CAPS/Introduction) hierarchy. +- `BIDS_DIRECTORY`, which is the input folder containing the dataset in a [BIDS](../BIDS.md) hierarchy; +- `CAPS_DIRECTORY`, which is the output folder containing the expected results in a [CAPS](../CAPS/Introduction.md) hierarchy. +It can be also the input folder containing the dataset in a [CAPS](../CAPS/Introduction.md) hierarchy. ### `GROUP_LABEL` You will see the `GROUP_LABEL` argument when working on any group-wise analysis (e.g. template creation from a list of subjects, statistical analysis). This is simply a label name that will define the group of subjects used for this analysis. -It will be written in your output [CAPS](../CAPS/Introduction) folder, for possible future reuses. +It will be written in your output [CAPS](../CAPS/Introduction.md) folder, for possible future reuses. For example, an `AD` group ID label could be used when creating a template for a group of Alzheimer’s disease patients. Any time you would like to use this `AD` template you will need to provide the group ID used to identify the pipeline output obtained from this group. You might also use `CNvsAD`, for instance, as group ID for a statistical group comparison between patients with Alzheimer's disease (`AD`) and cognitively normal (`CN`) subjects. -## Common options - -### `-tsv` / `--subjects_sessions_tsv` - -The `-tsv` flag allows you to specify in a TSV file the participants belonging to your subset. -For instance, running the [FreeSurfer pipeline](../Pipelines/T1_FreeSurfer) on T1w MRI can be done using : - -```shell -clinica run t1-freesurfer path/to/my/bids/dataset path/where/results/will/be/stored -tsv my_list_of_subjects.tsv -``` - -where your TSV file looks as follows: - -```text -participant_id session_id -sub-CLNC0001 ses-M000 -sub-CLNC0001 ses-M018 -sub-CLNC0001 ses-M036 -sub-CLNC0002 ses-M000 -sub-CLNC0002 ses-M018 -sub-CLNC0002 ses-M036 -sub-CLNC0003 ses-M000 -``` - - -### `-wd` / `--working_directory` - -In every pipeline, a working directory can be specified. -This directory gathers all the inputs and outputs of the different steps of the pipeline. -It is then very useful for the debugging process. -It is specially useful in the case where your pipeline execution crashes and you relaunch it with the exact same parameters, allowing you to continue from the last successfully executed node. - -For the pipelines that generate many files, such as `dwi-preprocessing` (especially if you run it on multiple subjects), a specific drive/partition with enough space can be used to store the working directory. - -### `-np` / `--n_procs` - -The `--n_procs` flag allows you to exploit several cores of your machine to run pipelines in parallel, which is very useful when dealing with numerous subjects and multiple sessions. -Thanks to [Nipype](https://nipype.readthedocs.io/en/latest/), even for a single subject, a pipeline can be run in parallel by exploiting the cores available to process simultaneously independent sub-parts. - -If you do not specify `-np` / `--n_procs` flag, Clinica will detect the number of threads to run in parallel and propose the adequate number of threads to the user. +--8<-- "snippets/pipelines_options.md" +--8<-- "snippets/converters_options.md" ## :warning: Known issues diff --git a/docs/Third-party.md b/docs/Software/Third-party.md similarity index 98% rename from docs/Third-party.md rename to docs/Software/Third-party.md index 1f7d5edfd..beb3cf748 100644 --- a/docs/Third-party.md +++ b/docs/Software/Third-party.md @@ -52,11 +52,14 @@ Please check the installation instructions for all platforms on [dcm2niix Git re
Some, but not all pipelines use specific third-party software. Depending on your usage of Clinica, you will need to install additional packages. -Specific dependencies are listed below (1) : +Specific dependencies are described in the table below (1) :
1. If not listed, the pipeline does not require any additional dependency outside Clinica. +??? info "Clinica available pipelines" + --8<-- "snippets/inventory_pipelines.md" +
| | ANTs | Convert3D | FreeSurfer | FSL | ITK | Matlab | MRtrix3 | PETPVC | SPM | diff --git a/docs/index.md b/docs/index.md index 26aef3119..72e7ccfad 100644 --- a/docs/index.md +++ b/docs/index.md @@ -14,8 +14,9 @@ We assume that users installing and using Clinica are comfortable using the comm -- [Installation](./Installation) -- [Third-party software](./Third-party) +- [Installation](Software/Installation.md) +- [Third-party software](Software/Third-party.md) +- [Interacting with Clinica](Software/InteractingWithClinica.md) bashcompinit source ~/.bash_completion.d/python-argcomplete.sh ``` + + +--8<-- "snippets/known_issues.md:matlab" diff --git a/docs/snippets/known_issues.md b/docs/snippets/known_issues.md new file mode 100644 index 000000000..c7857f50c --- /dev/null +++ b/docs/snippets/known_issues.md @@ -0,0 +1,9 @@ +--8<-- [start:matlab] +## :warning: Known issue with Matlab and SPM12 + +[Matlab](https://www.mathworks.com/products/matlab.html) and [SPM12](https://www.fil.ion.ucl.ac.uk/spm/software/spm12/) (whose implementation is based on Matlab) can sometimes randomly crash, causing a rather unreadable error in the console. +Those events are unpredictable. In case it occurs to you, please do the following: + +- Check that you have a valid Matlab license. +- Before relaunching the command line, be sure to remove the content of the working directory (if you specified one). +--8<-- [end:matlab] diff --git a/mkdocs.yml b/mkdocs.yml index b3deca76b..c8a01d9ad 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -74,10 +74,7 @@ markdown_extensions: alternate_style: True not_in_nav: | - /snippets/converters_options.md - /snippets/abbreviations.md - /snippets/inventory_converters.md - /snippets/inventory_pipelines.md + /snippets/ # Page tree nav: From 1462b4827a99325cba57a1ce1331d4e95c1c4698 Mon Sep 17 00:00:00 2001 From: AliceJoubert Date: Tue, 10 Sep 2024 18:04:18 +0200 Subject: [PATCH 5/6] Add tip --- docs/Software/InteractingWithClinica.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/docs/Software/InteractingWithClinica.md b/docs/Software/InteractingWithClinica.md index fdd44fc99..dca9cec35 100644 --- a/docs/Software/InteractingWithClinica.md +++ b/docs/Software/InteractingWithClinica.md @@ -46,7 +46,11 @@ If your dataset does not follow this standard, you will need to **convert it** : ## Clinica command-line interface Clinica's main usage is through command-line. -Clinica supports autocompletion: to see the list of commands, simply type `clinica` followed by ++tab++. + +!!! tip "See the list of available commands on your terminal" + - Do not hesitate to use `-h` or `--help` after any component of the command line, + ex : `clinica -h`, `clinica run -h` ... to see what options are available. + - Clinica supports autocompletion for zsh shell users : to see the list of commands, simply type `clinica` followed by ++tab++. In general, a Clinica command-line has the following syntax: From f1fb40c16c65dba9d59145eec6bec8431838e57c Mon Sep 17 00:00:00 2001 From: AliceJoubert Date: Wed, 11 Sep 2024 10:52:56 +0200 Subject: [PATCH 6/6] Changes upon suggestions --- docs/Software/Third-party.md | 9 +++++---- docs/index.md | 13 +++++-------- 2 files changed, 10 insertions(+), 12 deletions(-) diff --git a/docs/Software/Third-party.md b/docs/Software/Third-party.md index 8bb7ff990..53a0bde6b 100644 --- a/docs/Software/Third-party.md +++ b/docs/Software/Third-party.md @@ -295,15 +295,16 @@ export SPMSTANDALONE_HOME="/path/to/your/spmstandalone/home/" ___ -### Autocompletion +### Autocompletion (optional) - +```{ .bash .copy } +eval "$(register-python-argcomplete clinica)" +``` !!! warning "Autocompletion for `zsh` shell users" `zsh` shell users will have to add this right before the last line of their configuration file to enable autocompletion in Clinica: - ```bash + ```{ .bash .copy } autoload bashcompinit bashcompinit source ~/.bash_completion.d/python-argcomplete.sh diff --git a/docs/index.md b/docs/index.md index 72e7ccfad..51375572f 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,19 +1,16 @@ # Clinica Documentation -## [What is Clinica?](WhatIsClinica) +## 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). ## Installation -Clinica can be installed on Mac OS X and Linux (CentOS or Debian/Ubuntu) machines, +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) @@ -83,7 +80,7 @@ as well as the references mentioned on the wiki page of the pipelines you used. Each page includes text to cite the software packages that are used by Clinica (for example, citing SPM when using the `t1-volume` pipeline). -!!! info "Disclaimer" +!!! warning "Disclaimer" Clinica is a software for research studies. It is not intended for use in medical routine.