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CPP SPM

This is a set of functions to MRI analysis on a BIDS data set using SPM12.

Installation

We strongly recommend using the CPP fMRI analysis template repository (INSERT URL) to use CPP_SPM.

Download this repository and unzip the content where you want to install it.

Or clone the repo.

git clone --recurse-submodule https://github.com/cpp-lln-lab/CPP_SPM.git

Fire up Octave or Matlab and type

cd CPP_SPM

% The following adds the relevant folders to your path.
% This needs to be done once per session (your path will not be saved)

initCppSpm()

Please see our documentation for more detailed instructions.

Dependencies

Make sure that the following toolboxes are installed and added to the matlab path.

For instructions see the following links:

Dependencies	Used version
Matlab	20???
or octave	4.?
SPM12	>7219

Features

This can perform:

• slice timing correction,

• spatial preprocessing:

  • realignment, coregistration func to anat, anat segmentation, normalization to MNI space

  • realignm and unwarp, coregistration func to anat, anat segmentation

• smoothing,

• Quality analysis:

  • for anatomical data
  • for functional data

• GLM at the subject level

• GLM at the group level à la SPM (meaning using a summary statistics approach).

The core functions are in the src folder.

Please see our documentation for more info.

Octave compatibility

The following features do not yet work with Octave:

• anatomicalQA
• functionalQA
• slice_display toolbox

Contributing

Feel free to open issues to report a bug and ask for improvements.

If you want to contribute, have a look at our contributing guidelines that are meant to guide you and help you get started. If something is not clear or you get stuck: it is more likely we did not do good enough a job at explaining things. So do not hesitate to open an issue, just to ask for clarification.

Style guidelines

These are some of the guidelines we try to follow.

We use camelCase to name functions and variables for the vast majority of the code in this repository.

Scripts names in general and as well functions related to the demos use a snake_case.

Constant are written in UPPERCASE.

Pre-commit

There is a pre-commit hook that you can use to reformat files as you commit them.

Install pre-commit by using our requirements.txt file

pip install -r requirements.txt

Install the hook

pre-commit install

You're done. mh_style --fix will now be run every time you commit.

Contributors

Thanks goes to these wonderful people (emoji key):

CerenB 🐛 🖋 📖 💻 👀	Fede F. 🐛	Michèle MacLean 💻 🤔	Mohamed Rezk 💻 👀 🎨	OliColli 💻 🎨 📖	Remi Gau 💻 📖 🚇 🎨 👀 🐛 ⚠️	anege 💻 🎨
marcobarilari 💻 🎨 👀 📖 ⚠️ 🐛

This project follows the all-contributors specification. Contributions of any kind welcome!