This is a set of functions to prepare a source fMRI dataset for BIDSification and analyses
This can perform:
-
3D to 4D nii files conversion
-
anatomical defacing [ W I P ]
-
gzip the nii files in a BIDS raw folder
The core functions are in the src folder. This set of functions is intended to be added manually
as a submodule to the analysis repo forked from
template_fMRI_analysis
-
Open the terminal and navigate to your analysis folder forked from template_fMRI_analysis and cloned locally
-
Type
# navigate to the `lib` folder
cd lib
# add the submodule
git submodule add https://github.com/cpp-lln-lab/CPP_sourceMRI
# initialize the nested submodule(s)
git submodule update --init --recursive- commit the new changes (the new submodule(s))
Make sure that the following toolboxes are installed path.
For instructions see the following links:
| Dependencies | Used version |
|---|---|
| Matlab | 20??? |
| or octave | 4.? |
| SPM12 | v7487 |
| CPP_SPM* | > 0.1.0 |
*already "installed" in template_fMRI_analysis and cloned locally
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.