Expand git section

Author: gllmflndn

docs/assets/figures/git_clone_repo.png

@@ -59,6 +59,11 @@ The instructions to set your commit name and email address in GitHub Desktop are
 
 * [Configuring your global author information](https://docs.github.com/en/desktop/installing-and-configuring-github-desktop/configuring-and-customizing-github-desktop/configuring-git-for-github-desktop#configuring-your-global-author-information)
 
+<figure markdown>
+  ![Git configuration](../assets/figures/git_config.png)
+  <figcaption>Specify your commit name and email address in GitHub Desktop.</figcaption>
+</figure>
+
 The command line equivalent is:
 
 ```
@@ -94,7 +99,12 @@ To apply this setting from GitHub Desktop, you need to open the command prompt b
 
 ## Clone the SPM repository
 
-Follow [these instructions](https://docs.github.com/en/desktop/contributing-and-collaborating-using-github-desktop/adding-and-cloning-repositories/cloning-a-repository-from-github-to-github-desktop) with the SPM repository: https://github/spm/spm
+Follow [these instructions](https://docs.github.com/en/desktop/contributing-and-collaborating-using-github-desktop/adding-and-cloning-repositories/cloning-a-repository-from-github-to-github-desktop) with the SPM repository: [https://github/spm/spm](https://github/spm/spm)
+
+<figure markdown>
+  ![Git clone](../assets/figures/git_clone_repo.png)
+  <figcaption>Clone the SPM repository from its GitHub URL.</figcaption>
+</figure>
 
 From the command line, the equivalent is:
 
@@ -104,7 +114,20 @@ git clone [email protected]:spm/spm.git
 
 ## Git Commits
 
-### Log Messages
+After editing some files in the `main` branch, select the changes to include in a commit, write a commit message and push the changes to `origin`:
+
+* [Making changes](https://docs.github.com/en/desktop/contributing-and-collaborating-using-github-desktop/making-changes-in-a-branch/committing-and-reviewing-changes-to-your-project#selecting-changes-to-include-in-a-commit)
+
+From the command line, this is obtained with:
+
+```
+git add spm_example.m
+git commit -m "<commit message>"
+```
+
+Ideally, "each commit should be a perfect, atomic unit of change". Do commit related changes, commit often but don't commit half-done work (use branch or stash instead).
+
+### Commit Messages
 
 Use the imperative and prefix the commit message with one of:
 
@@ -114,6 +137,18 @@ Use the imperative and prefix the commit message with one of:
 * ++"Documentation"++
 * ++"Refactoring"++
 
+You should be able to suffix a commit message to the phrase "If applied, this code will ...".
+
+Commit messages should begin with a short summary of the changes (up to 70 characters) followed by a blank line and the body text, i.e.:
+
+```
+Enhancement: replace this with that in such and such
+
+Longer description that might contain bullet points:
+* item 1
+* item 2
+```
+
 ## Git Workflow
 
 We are using a [Centralised Workflow](https://www.atlassian.com/git/tutorials/comparing-workflows#centralized-workflow). This is also called [Trunk Based Development](https://trunkbaseddevelopment.com/) (see this [article](https://medium.com/@mattia.battiston/why-i-love-trunk-based-development-641fcf0b94a0) for a discussion). Popular other workflows include [GitHub Flow](https://githubflow.github.io/) and [Gitflow](https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow).
@@ -122,7 +157,6 @@ We are using a [Centralised Workflow](https://www.atlassian.com/git/tutorials/co
 
 Recommendation for pull request reviewers: When merging, we generally like `squash+merge`. Unless it is the rare case of a PR with carefully staged individual commits that you want in the history separately, in which case `merge` is acceptable, but usually prefer `squash+merge`.
 
-
 ## References
 
 * [Dangit, Git!?!](https://dangitgit.com/)

docs/assets/figures/git_config.png

@@ -4,14 +4,12 @@
     The SPM software is a collection of [MATLAB](https://www.mathworks.com/products/matlab.html) functions and thus requires the MATLAB software to be installed on your computer in order to run. SPM requires only core MATLAB to run (no special toolboxes are required - unless stated otherwise).
 
     Each SPM version was written for a particular MATLAB version and will not work with earlier versions. MATLAB versions released after SPM can have some peculiarities but SPM developers try to provide compatibility fixes in the updates.
-    
-    [GNU Octave](https://www.octave.org/) is a free open-source numerical analysis software similar to MATLAB. See SPM/Octave for more details about compatibility between SPM and Octave.
 
 === "Windows"
 
     ## Installation
 
-    1. Download spm12.zip.
+    1. Download `spm12.zip` from the [SPM website](https://www.fil.ion.ucl.ac.uk/spm/software/download/).
     2. Unzip spm12.zip in a folder of your choice, such as `C:\Users\login\Documents\MATLAB\spm12`.
     3. Start MATLAB and add SPM into your path, either using:
 
@@ -51,13 +49,12 @@
 
     Mac Intel with 64bit MATLAB is a supported SPM platform. Precompiled MEX files (`*.mexmaci64`) are included in the SPM distribution.
 
-    1. [Download `spm12.zip`](https://www.fil.ion.ucl.ac.uk/spm/software/download/) and its updates `spm12_updates_rxxxx.zip` in your home directory.
+    1. [Download `spm12.zip`](https://www.fil.ion.ucl.ac.uk/spm/software/download/) in your home directory.
 
     2. Uncompress the archive by typing the following in a terminal:
         ```
         cd /Users/login
         unzip spm12.zip
-        unzip -o spm12_updates_rxxxx.zip -d spm12
         ```
 
     3. Start MATLAB and add SPM to your path, either using: 
@@ -138,14 +135,13 @@
 
     ## Installation
 
-    1. Download `spm12.zip` and its updates `spm12_updates_rxxxx.zip` in your home directory.
+    1. [Download `spm12.zip`](https://www.fil.ion.ucl.ac.uk/spm/software/download/) in your home directory.
 
     2. Uncompress the archive by typing the following in a terminal:
 
         ```
         cd /home/login
         unzip spm12.zip
-        unzip -o spm12_updates_rxxxx.zip -d spm12
         ```
 
     3. Start MATLAB and add SPM into your path, either using:

docs/development/git.md

@@ -9,15 +9,11 @@ Normalisation refers to bringing your data into a standard template space to all
 
     For a thorough overview of issues related to normalisation, see the SPM book:
 
-    [Penny, W., Friston, K., Ashburner, J., Kiebel, S., & Nichols, T. (2006). *Statistical parametric mapping: The analysis of functional brain images* (1st ed.).](http://www.elsevierdirect.com/product.jsp?isbn=9780123725608&srccode=89660)
+    [Penny, W., Friston, K., Ashburner, J., Kiebel, S., & Nichols, T. (2006). *Statistical parametric mapping: The analysis of functional brain images*.](https://www.fil.ion.ucl.ac.uk/spm/doc/#books)
 
     And other readings:
 
-    [Brett, M., Johnsrude, I. S., & Owen, A. M. (2002). The problem of functional localization in the human brain. *Nature Reviews Neuroscience, 3*(3), 243-249.](https://doi.org/10.1038/nrn756)
-
-    [Jenkinson, M. & Chappell, M. (2018). *Introduction to neuroimaging analysis*. Oxford University Press.](http://www.neuroimagingprimers.org/examples/introduction-primer-example-boxes/)
-
-    [Poldrack, R. A., Mumford, J. A., & Nichols, T. E. (2011). *Handbook of functional MRI data analysis*. Cambridge University Press.](https://www.cambridge.org/core/books/handbook-of-functional-mri-data-analysis/8EDF966C65811FCCC306F7C916228529)
+    [Ashburner, J. and Firston, K.J. (2005) *Unified segmentation*.](https://doi.org/10.1016/j.neuroimage.2005.02.018)
 
 1. From the SPM menu panel, select `Normalise (Write)`. You will see a pop-up window appear looking like this:
 

docs/installation.md

@@ -9,13 +9,7 @@ Realignment refers to correcting the functional data for movement that has occur
 
     For a thorough overview of issues related to motion in fMRI, see the SPM book:
 
-    [Penny, W., Friston, K., Ashburner, J., Kiebel, S., & Nichols, T. (2006). *Statistical parametric mapping: The analysis of functional brain images* (1st ed.).](http://www.elsevierdirect.com/product.jsp?isbn=9780123725608&srccode=89660)
-
-    And other readings:
-
-    [Jenkinson, M. & Chappell, M. (2018). *Introduction to neuroimaging analysis*. Oxford University Press.](http://www.neuroimagingprimers.org/examples/introduction-primer-example-boxes/)
-
-    [Poldrack, R. A., Mumford, J. A., & Nichols, T. E. (2011). *Handbook of functional MRI data analysis*. Cambridge University Press.](https://www.cambridge.org/core/books/handbook-of-functional-mri-data-analysis/8EDF966C65811FCCC306F7C916228529)
+    [Penny, W., Friston, K., Ashburner, J., Kiebel, S., & Nichols, T. (2006). *Statistical parametric mapping: The analysis of functional brain images*.](https://www.fil.ion.ucl.ac.uk/spm/doc/#books)
 
 1. From the SPM menu panel, select `Realign (Estimate & Reslice)`. You will see a pop-up window appear looking like this:
 

docs/tutorials/fmri_preprocessing/normalisation.md

@@ -17,13 +17,11 @@ Slice timing correction aims to account for the differences in timing of data ac
 
     For a thorough overview of issues related to slice timing in fMRI, see the SPM book:
 
-    [Penny, W., Friston, K., Ashburner, J., Kiebel, S., & Nichols, T. (2006). *Statistical parametric mapping: The analysis of functional brain images* (1st ed.).](http://www.elsevierdirect.com/product.jsp?isbn=9780123725608&srccode=89660)
+    [Penny, W., Friston, K., Ashburner, J., Kiebel, S., & Nichols, T. (2006). *Statistical parametric mapping: The analysis of functional brain images*.](https://www.fil.ion.ucl.ac.uk/spm/doc/#books)
 
     And other readings:
 
-    [Jenkinson, M. & Chappell, M. (2018). *Introduction to neuroimaging analysis*. Oxford University Press.](http://www.neuroimagingprimers.org/examples/introduction-primer-example-boxes/)
-
-    [Poldrack, R. A., Mumford, J. A., & Nichols, T. E. (2011). *Handbook of functional MRI data analysis*. Cambridge University Press.](https://www.cambridge.org/core/books/handbook-of-functional-mri-data-analysis/8EDF966C65811FCCC306F7C916228529)
+    [Sladky, R., Friston, K.j., Trostl J., Cunnington, R., Moser, E, Windischberger, C. (2011). *Slice-timing effects and their correction in functional MRI*.](https://doi.org/10.1016/j.neuroimage.2011.06.078)
 
 ??? info "When to use slice timing correction?"
     * Slice timing can be done on any fMRI data but it is particularly beneficial for studies with **longer TRs** (i.e. >2s). For studies with shorter TRs (≤2s), temporal derivative may be a better option.

docs/tutorials/fmri_preprocessing/realignment.md

@@ -9,13 +9,7 @@ Smoothing is the process of averaging the signal in each voxel with a weighted a
 
     For a thorough overview of issues related to smoothing, see the SPM book:
 
-    [Penny, W., Friston, K., Ashburner, J., Kiebel, S., & Nichols, T. (2006). *Statistical parametric mapping: The analysis of functional brain images* (1st ed.).](http://www.elsevierdirect.com/product.jsp?isbn=9780123725608&srccode=89660)
-
-    And other readings:
-
-    [Jenkinson, M. & Chappell, M. (2018). *Introduction to neuroimaging analysis*. Oxford University Press.](http://www.neuroimagingprimers.org/examples/introduction-primer-example-boxes/)
-
-    [Poldrack, R. A., Mumford, J. A., & Nichols, T. E. (2011). *Handbook of functional MRI data analysis*. Cambridge University Press.](https://www.cambridge.org/core/books/handbook-of-functional-mri-data-analysis/8EDF966C65811FCCC306F7C916228529)
+    [Penny, W., Friston, K., Ashburner, J., Kiebel, S., & Nichols, T. (2006). *Statistical parametric mapping: The analysis of functional brain images*.](https://www.fil.ion.ucl.ac.uk/spm/doc/#books)
 
 1. From the SPM menu panel, select `Smooth`. You will see a pop-up window appear looking like this:
 

docs/tutorials/fmri_preprocessing/slice_timing.md

@@ -5,17 +5,17 @@
 Let's take a look at the structure of the data you [downloaded](https://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip). The data is organised following [BIDS](https://bids.neuroimaging.io/) - a standardised format for organising and naming neuroimaging files, and looks like this:
 
 ``` 
-MoAEpilot/
-    CHANGES
-    dataset_description.json
-    README
-    sub-01/
-        anat/
-            sub-01_T1w.nii
-        func/
-            sub-01_task-auditory_bold.nii
-            sub-01_task-auditory_events.tsv
-    task-auditory_bold.json
+MoAEpilot
+├── CHANGES
+├── dataset_description.json
+├── README
+├── sub-01
+│   ├── anat
+│   │   └── sub-01_T1w.nii
+│   └── func
+│       ├── sub-01_task-auditory_bold.nii
+│       └── sub-01_task-auditory_events.tsv
+└── task-auditory_bold.json
 ```
 
 Inside the folder containing the Mother of All Experiments (MoAE) data, you can find `CHANGES`, `dataset_description.json`, `README` and `task-auditory_bold.json` files - these files contain meta-data about the study. The subject directory, `sub-01`, contains `anat` and `func` folders, which store anatomical and functional images, respectively. Additionally, onset timings for task data are stored in the `func` folder alongside task images. 
@@ -28,13 +28,13 @@ We will first look at the anatomical image `sub-01_T1w.nii` stored in `sub-01/an
 
 From your terminal or Matlab window open SPM by typing:
 
-```
+```matlab
 spm fmri
 ```
 
 or:
 
-```
+```matlab
 spm
 ```
 
@@ -43,8 +43,8 @@ and selecting `fMRI` in the SPM window.
 To view an image, click on `Display` from the SPM menu and select the image you want to inspect from the pop-up window. The selected image will now be shown in the SPM graphics window. 
 
 !!! tip "File extensions"
-    SPM can read read files in the Analyze format (`.hdr`/`.img`) and uncompressed NIFTI files (`.nii`). If your files are compressed and end in `.gz`, make sure to uncompress them first, e.g.:
-    ```
+    SPM can read uncompressed NIfTI files in single (`.nii`) and dual (`.hdr`/`.img`) formats. If your files are compressed with `gzip` and end in `.gz`, make sure to uncompress them first, e.g.:
+    ```matlab
     gunzip your_file.nii.gz
     ```