[DOC] Remove parts about SPM + MATLAB set-up from the documentation. (aramis-lab#1622)

AliceJoubert · web-flow · commit a99b04ad3af2 · 2026-02-03T10:39:33.000+01:00
* Remove SPM + MATLAB mentions

* Test for spacing

* Test for spacing 2

* Test spacing table 3

* Adjust table size

* Change column size in css

* Try2

* Update css 3

* Final fix on css

* Modify name
diff --git a/docs/CAPS/Specifications.md b/docs/CAPS/Specifications.md
@@ -64,9 +64,9 @@ subjects/
                   └─ <source_file>_segm-<segm>_dartelinput.nii.gz
 ```
 
-- 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 `modulated-{on|off}` key indicates if modulation has been used in [SPM](../Software/Third-party.md#spm-standalone) 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](../Software/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#spm-standalone) segmentation routine to the T1 image in native space.
 
 #### DARTEL
 
@@ -81,7 +81,7 @@ 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](../Software/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#spm-standalone) DARTEL existing templates procedure).
 
 !!! Note "Note for SPM experts"
     The original name of `<group_id>_iteration-<index>_template.nii.gz` is `Template<index>.nii`.
diff --git a/docs/IOTools/center_nifti.md b/docs/IOTools/center_nifti.md
@@ -1,7 +1,7 @@
 # `center-nifti` - Center NIfTI files of a BIDS directory
 
 Your [BIDS](http://bids.neuroimaging.io) dataset may contain NIfTI files where the origin does not correspond to the center of the image (i.e. the anterior commissure).
-[SPM](../Software/Third-party.md#spm12) is especially sensitive to this case and segmentation procedures may result in blank images or even fail.
+[SPM](../Software/Third-party.md#spm-standalone) is especially sensitive to this case and segmentation procedures may result in blank images or even fail.
 To mitigate this issue we offer a simple tool that generates from your BIDS a new dataset with centered NIfTI files for the selected modalities.
 
 
diff --git a/docs/Pipelines/PET_Surface.md b/docs/Pipelines/PET_Surface.md
@@ -1,7 +1,5 @@
 <!-- markdownlint-disable MD033 MD046 -->
 
---8<-- "snippets/spm_banner.md"
-
 # `pet-surface` - Surface-based processing of PET images
 
 This pipeline performs several processing steps for the analysis of PET data on the cortical surface [[Marcoux et al., 2018](https://doi.org/10.3389/fninf.2018.00094)]:
@@ -25,9 +23,7 @@ You need to have performed the [`t1-freesurfer`](./T1_FreeSurfer.md) pipeline on
 
 ## Dependencies
 
-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](../Software/Third-party.md#spm12) and [Matlab](../Software/Third-party.md#matlab), or [spm standalone](../Software/Third-party.md#spm12-standalone).
+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 install [spm standalone](../Software/Third-party.md#spm-standalone).
 
 ## Running the pipeline
 
diff --git a/docs/Pipelines/PET_Surface_Longitudinal.md b/docs/Pipelines/PET_Surface_Longitudinal.md
@@ -1,7 +1,5 @@
 <!-- markdownlint-disable MD046 -->
 
---8<-- "snippets/spm_banner.md"
-
 # `pet-surface-longitudinal` - Surface-based longitudinal processing of PET images
 
 This pipeline performs several processing steps for the longitudinal analysis of PET data on the cortical surface
@@ -30,9 +28,7 @@ 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](../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](../Software/Third-party.md#spm12) and [Matlab](../Software/Third-party.md#matlab), or [spm standalone](../Software/Third-party.md#spm12-standalone).
+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 install [spm standalone](../Software/Third-party.md#spm-standalone).
 
 
 ## Running the pipeline
diff --git a/docs/Pipelines/PET_Volume.md b/docs/Pipelines/PET_Volume.md
@@ -1,7 +1,5 @@
 <!-- markdownlint-disable MD046 -->
 
---8<-- "snippets/spm_banner.md"
-
 # `pet-volume` – Volume-based processing of PET images
 
 This pipeline performs several processing steps on [PET](../glossary.md#pet) data in voxel space, which include:
@@ -23,7 +21,7 @@ You need to have performed the [`t1-volume`](./T1_Volume.md) pipeline on your T1
 
 ## Dependencies
 
-If you only installed the core of Clinica, this pipeline needs the installation of [SPM standalone](../Software/Third-party.md#spm12-standalone).
+If you only installed the core of Clinica, this pipeline needs the installation of [SPM standalone](../Software/Third-party.md#spm-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](../Software/Third-party.md#petpvc), which depends on [ITK 4](../Software/Third-party.md#itk).
 
diff --git a/docs/Pipelines/Stats_Volume.md b/docs/Pipelines/Stats_Volume.md
@@ -1,6 +1,5 @@
 <!-- markdownlint-disable MD046 -->
 
---8<-- "snippets/spm_banner.md"
 
 # `statistics-volume` - Volume-based mass-univariate analysis with SPM
 
@@ -12,7 +11,7 @@ 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](../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.
+If you only installed the core of Clinica, this pipeline needs the installation of [SPM standalone](../Software/Third-party.md#spm-standalone), on your computer.
 
 ## Running the pipeline
 
diff --git a/docs/Pipelines/T1_Volume.md b/docs/Pipelines/T1_Volume.md
@@ -1,7 +1,5 @@
 <!-- markdownlint-disable MD007 MD033 -->
 
---8<-- "snippets/spm_banner.md"
-
 # `t1-volume` – Volume-based processing of T1-weighted MR images with SPM
 
 This pipeline performs four main processing steps on T1-weighted MR images using the [SPM](http://www.fil.ion.ucl.ac.uk/spm/) software:
@@ -26,7 +24,7 @@ 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 [SPM standalone](../Software/Third-party.md#spm12-standalone) on your computer.
+If you only installed the core of Clinica, this pipeline needs the installation of [SPM standalone](../Software/Third-party.md#spm-standalone) on your computer.
 
 ## Running the pipeline
 
diff --git a/docs/Software/Third-party.md b/docs/Software/Third-party.md
@@ -1,7 +1,5 @@
 <!-- markdownlint-disable MD046 -->
 
---8<-- "snippets/spm_banner.md"
-
 # Third-party software
 
 ## Environment variables set-up
@@ -65,20 +63,19 @@ Specific dependencies are described in the table below (1) :
 
 <div markdown="1" class="third_party_table">
 
-|                     | ANTs | Convert3D | FreeSurfer | FSL | ITK | Matlab | MRtrix3 | PETPVC | SPM |
-|:-------------------:|:----:|:---------:|:----------:|:---:|:---:|:------:|:-------:|:------:|:---:|
-|    Anat > Linear    |  ✓∘  |           |            |     |     |        |         |        |     |
-|    Anat > Volume    |      |           |            |     |     |   ✓    |         |        |  ✓  |
-|  Anat > FreeSurfer  |      |           |     ✓      |     |     |        |         |        |     |
-| DWI > Preprocessing |  ✓   |     ✓     |            |  ✓  |     |        |    ✓    |        |     |
-|      DWI > DTI      |  ✓   |           |            |  ✓  |     |        |    ✓    |        |     |
-|  DWI > Connectome   |      |           |     ✓      |  ✓  |     |        |    ✓    |        |     |
-|    PET > Linear     |  ✓   |           |            |     |     |        |         |        |     |
-|    PET > Surface    |      |           |     ✓      |  ✓  | ✓⟡  |   ✓    |         |   ✓⟡   |  ✓  |
-|    PET > Volume     |      |           |            |     | ✓⟡  |   ✓    |         |   ✓⟡   |  ✓  |
-|   Stats > Surface   |      |           |     ✓      |     |     |        |         |        |     |
-|   Stats > Volume    |      |           |            |     |     |   ✓    |         |        |  ✓  |
-
+|                     | ANTs  | Convert3D | FreeSurfer | FSL | ITK | MRtrix3 | PETPVC | SPM |
+|:-------------------:|:-----:|:---------:|:----------:|:---:|:---:|:-------:|:------:|:---:|
+|    Anat > Linear    |  ✓∘   |           |            |     |     |         |        |     |
+|    Anat > Volume    |       |           |            |     |     |         |        |  ✓  |
+|  Anat > FreeSurfer  |       |           |     ✓      |     |     |         |        |     |
+| DWI > Preprocessing |   ✓   |     ✓     |            |  ✓  |     |    ✓    |        |     |
+|      DWI > DTI      |   ✓   |           |            |  ✓  |     |    ✓    |        |     |
+|  DWI > Connectome   |       |           |     ✓      |  ✓  |     |    ✓    |        |     |
+|    PET > Linear     |   ✓   |           |            |     |     |         |        |     |
+|    PET > Surface    |       |           |     ✓      |  ✓  | ✓⟡  |         |   ✓⟡   |  ✓  |
+|    PET > Volume     |       |           |            |     | ✓⟡  |         |   ✓⟡   |  ✓  |
+|   Stats > Surface   |       |           |     ✓      |     |     |         |        |     |
+|   Stats > Volume    |       |           |            |     |     |         |        |  ✓  |
 </div>
 
 - *✓∘ : for anatomical linear pipelines there is also the possibility to use ANTsPy instead of ANTs since Clinica `v0.9.0`* 
@@ -202,23 +199,6 @@ official instructions for [downloading](https://www.mrtrix.org/download/).
 
 ___
 
-### Matlab
-
-You can find more details about `Matlab` on their [website](https://fr.mathworks.com/products/matlab/).
-
-!!! warning
-    Note that using `Matlab` requires having a **valid license** which might be available through your university or institution.
-
-Make sure to have the following environment variables defined:
-
-```{ .bash .copy }
-export MATLAB_HOME="/path/to/your/matlab/bin/"
-export PATH=${MATLAB_HOME}:${PATH}
-export MATLABCMD="${MATLAB_HOME}/matlab"
-```
-
-___
-
 ### PETPVC
 
 You can find more details about `PETPVC` on their [website](https://github.com/UCL/PETPVC),
@@ -235,59 +215,16 @@ You have basically three options:
 
 ___
 
-### SPM12
-
-!!! warning "SPM12 and Matlab"
-    Note that `SPM12` works with [Matlab](#matlab) such that Clinica pipelines which require `SPM12`, will also need a `Matlab` installation.
-    If you cannot install `Matlab`, you can install [SPM standalone](#spm12-standalone).
-
-You can find more details about `SPM12` on their [website](http://www.fil.ion.ucl.ac.uk/spm/). To install it :
-
-=== "Linux"
-    Download the latest version [here](http://www.fil.ion.ucl.ac.uk/spm/download/restricted/eldorado/spm12.zip) and follow the instructions on the [SPM wiki](https://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Linux).
-
-=== "MacOS"
-    Download the latest version [here](http://www.fil.ion.ucl.ac.uk/spm/download/restricted/eldorado/spm12.zip) and follow the instructions on the [SPM wiki](https://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Mac_OS_(Intel)).
-
-    ??? 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.
+### SPM Standalone
 
-Then :
+!!! danger "Set-up MATLAB + SPM"
+    Clinica now only supports SPM standalone, which functions without MATLAB.
 
-1. Make sure to have the following environment variable defined:
-    ```{ .bash .copy }
-    export SPM_HOME="/path/to/your/spm12"
-    ```
+To use SPM standalone, you will need to install two things:
 
-   2. You must also add `SPM` to the `MATLAB` path variable if you installed it as a toolbox.
-      - First, verify a `startup.m` file exists in your *initial working folder*, by default `~/Documents/MATLAB` (see [here](https://fr.mathworks.com/help/matlab/ref/startup.html) for more details). 
-        If the file does not exist, you can create it.
-      - Then, type inside:
-       ```matlab
-       addpath('/path/to/your/spm12');
-       ```
-       **OR**, assuming the `$SPM_HOME` environment variable is set in your `~/.bashrc` file :
-       ```matlab
-       [~, spmhome] = system('source ~/.bashrc > /dev/null; echo $SPM_HOME;');
-       spmhome = strsplit(spmhome,'\n');
-       addpath(spmhome{end-1});
-       ```
-
-    !!! warning
-        `zsh` shell users will have to replace `~/.bashrc` by `~/.zshrc`.
-
-___
-
-### SPM12 standalone
-
-If you want to install `SPM12` without installing [Matlab](#matlab), you will need to install two things:
-
-- The Matlab runtime (often abbreviated into MCR), for which no license is required.
+- The Matlab Runtime (often abbreviated into MCR), for which no license is required.
 - The SPM standalone itself.
 
-!!! danger "Which version to use ?"
-    SPM has recently released a version `SPM25` on Github for which the installation is described [here](https://www.fil.ion.ucl.ac.uk/spm/docs/installation/standalone/).
-    Clinica does support this version for both `t1-volume` and `pet-volume`
 
 !!! tip "Verify your environment variables"
     If you followed the installation instructions, you should have set the environment variable `$LD_LIBRARY_PATH` on Linux, or `$DYLD_LIBRARY_PATH` on MacOS.
@@ -297,11 +234,9 @@ In addition, you need to define the following environment variables:
 ```bash
 export MCR_HOME="/path/to/your/MCR/"
 export SPMSTANDALONE_HOME="/path/to/your/spmstandalone/home/"
-export SPM_HOME="/path/to/your/spmstandalone/home/"
 ```
 
-!!! tip "Which paths to use ?"
-    - `SPM_HOME` is not actually used with this set-up but it still needs to be defined
+!!! tip "What are these paths ?"
     - `SPMSTANDALONE_HOME` should indicate the directory containing the `run_spmxx.sh` file.
     - `MCR_HOME` should indicate the directory containing the `bin`, `runtime`... folders
 
@@ -321,6 +256,3 @@ eval "$(register-python-argcomplete clinica)"
     bashcompinit
     source ~/.bash_completion.d/python-argcomplete.sh
     ```
-
-
---8<-- "snippets/known_issues.md:matlab"
diff --git a/docs/css/clinica.css b/docs/css/clinica.css
@@ -75,32 +75,29 @@ h3, .h3, .md-typeset h3 {
     }
 
 .third_party_table th:nth-child(1) {
-    width: 20%;
+    width: 19%;
     }
 .third_party_table th:nth-child(2) {
-    width: 8%;
+    width: 10%;
     }
 .third_party_table th:nth-child(3) {
-    width: 11%;
+    width: 15%;
     }
 .third_party_table th:nth-child(4) {
-    width: 11%;
+    width: 15%;
     }
 .third_party_table th:nth-child(5) {
-    width: 6%;
+    width: 7%;
     }
 .third_party_table th:nth-child(6) {
-    width: 6%;
+    width: 7%;
     }
     .third_party_table th:nth-child(7) {
-    width: 10%;
+    width: 12%;
     }
 .third_party_table th:nth-child(8) {
-    width: 10%;
+    width: 13%;
     }
 .third_party_table th:nth-child(9) {
-    width: 10%;
-    }
-.third_party_table th:nth-child(10) {
     width: 8%;
     }
diff --git a/docs/snippets/known_issues.md b/docs/snippets/known_issues.md
@@ -1,14 +1,3 @@
---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]
-
-
 --8<-- [start:center-nifti]
 !!! warning "Centering BIDS nifti"
     If the images from the `BIDS_DIRECTORY` are not centered, Clinica will give a **warning** because this can be an issue **if** later processing steps involve SPM (for instance if you are planning to run [pet-surface](./PET_Surface.md) afterwards).
diff --git a/docs/snippets/spm_banner.md b/docs/snippets/spm_banner.md

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`75`	`75`	`}`
`76`	`76`
`77`	`77`	`.third_party_table th:nth-child(1) {`
`78`		`- width: 20%;`
	`78`	`+ width: 19%;`
`79`	`79`	`}`
`80`	`80`	`.third_party_table th:nth-child(2) {`
`81`		`- width: 8%;`
	`81`	`+ width: 10%;`
`82`	`82`	`}`
`83`	`83`	`.third_party_table th:nth-child(3) {`
`84`		`- width: 11%;`
	`84`	`+ width: 15%;`
`85`	`85`	`}`
`86`	`86`	`.third_party_table th:nth-child(4) {`
`87`		`- width: 11%;`
	`87`	`+ width: 15%;`
`88`	`88`	`}`
`89`	`89`	`.third_party_table th:nth-child(5) {`
`90`		`- width: 6%;`
	`90`	`+ width: 7%;`
`91`	`91`	`}`
`92`	`92`	`.third_party_table th:nth-child(6) {`
`93`		`- width: 6%;`
	`93`	`+ width: 7%;`
`94`	`94`	`}`
`95`	`95`	`.third_party_table th:nth-child(7) {`
`96`		`- width: 10%;`
	`96`	`+ width: 12%;`
`97`	`97`	`}`
`98`	`98`	`.third_party_table th:nth-child(8) {`
`99`		`- width: 10%;`
	`99`	`+ width: 13%;`
`100`	`100`	`}`
`101`	`101`	`.third_party_table th:nth-child(9) {`
`102`		`- width: 10%;`
`103`		`- }`
`104`		`-.third_party_table th:nth-child(10) {`
`105`	`102`	`width: 8%;`
`106`	`103`	`}`