CPP SPM

This is a Matlab / Octave toolbox to perform MRI data analysis on a BIDS data set using SPM12.

Installation

Please see our documentation for more info.

Features

Preprocessing

If your data is fairly "typical" (for example whole brain coverage functonal data with one associated anatomical scan for each subject), you might be better off running fmriprep on your data.

If you have more exotic data that can't be handled well by fmriprep then CPP_SPM has some automated workflows to perform amongst other things:

• slice timing correction

• fieldmaps processing and voxel displacement map creation (work in progress)

• spatial preprocessing:

  • realignment OR realignm and unwarp
  • coregistration func to anat,
  • anat segmentation and skull stripping
  • (optional) normalization to SPM's MNI space

• smoothing

All preprocessed outputs are saved as BIDS derivatives with BIDS compliant filenames.

Statistics

The model specification are done via the BIDS stats model and can be used to perform:

• whole GLM at the subject level
• whole brain GLM at the group level à la SPM (meaning using a summary statistics approach).
• ROI based GLM (using marsbar)
• model selection (with the MACS toolbox)

Quality control:

• functional data (work in progress)
• GLM auto-correlation check

Please see our documentation for more info.

Citation

    @software{CPP_SPM,
        author = {Gau, Rémi and Barilari, Marco and Battal, Ceren and Rezk, Mohamed and Collignon, Olivier and Gurtubay, Ane and Falagiarda, Federica and MacLean, Michèle and Cerpelloni, Filippo},
        license = {GPL-3.0},
        title = {{CPP SPM}},
        url = {https://github.com/cpp-lln-lab/CPP_SPM},
        version = {1.1.3dev}
    }

Contributors

Thanks goes to these wonderful people (emoji key):

CerenB 🐛 🖋 📖 💻 👀 📓	Fede F. 🐛 📓	Filippo Cerpelloni 🐛 ⚠️ 📓	Iqra Shahzad 🐛 📖 💬 👀 📓	Michèle MacLean 💻 🤔 📓	Mohamed Rezk 💻 👀 🎨	OliColli 💻 🎨 📖
Remi Gau 💻 📖 🚇 🎨 👀 🐛 ⚠️	anege 💻 🎨	marcobarilari 💻 🎨 👀 📖 ⚠️ 🐛 📓

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