In this blog post, I describe how you can build your own standalone C++ program to analyze nii data without any dependencies beyond C++. Hence, it will work without the libraries from other fMRI software packages, e.g. odin, afni. The only tricky part is to use a stand alone nii I/O to write your own C++ evaluation programs. Here, I do it by incorporating the few files that i borrowed from the afni source code.
- Manual aligment of MP2RAGE with EPI (optional when MP2RAGE is acquired in same session)
- ANTS alignment of MP2RAGE and EPI. (part of anatomical_maser.sh, see github)
- Running Freesurfer on MP2RAGE data in EPI space. (part of anatomical_maser.sh, see github)
- Using SUMA to get fine samples tissue borders in EPI-voxel space (in oblique space) (part of anatomical_maser.sh, see github)
- Manual correction of Freesurfer GM-ribbon
- calculating layers from GM-ribbon in neuroDebian.
This is a description on how to use SPM and/or AFNI for high-resolution SS-SI-VASO data evaluations.
Here it is explained what to do with the raw fMTR data from the scanner to obtain CBV and BOLD signal time courses .
Every other image has a different contrast.