Using a standalone Nifti I/O in C++

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.

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Getting layers in EPI space


Big steps:

  1. Manual aligment of MP2RAGE with EPI (optional when MP2RAGE is acquired in same session)
  2. ANTS alignment of MP2RAGE and EPI. (part of, see github)
  3. Running Freesurfer on MP2RAGE data in EPI space. (part of, see github)
  4. Using SUMA to get fine samples tissue borders in EPI-voxel space (in oblique space) (part of, see github)
  5. Manual correction of Freesurfer GM-ribbon
  6. calculating layers from GM-ribbon in neuroDebian.

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Motion and BOLD correction in SS-SI-VASO


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.

Screenshot 2017-11-25 15.27.14.png

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