The code is on Github.

With a Linux/Mac set up for development (git and C compiler installed) you should be able to download and compile with the commands:

git clone https://github.com/rordenlab/dcm2niix.gi...
cd dcm2niix/console
make

To change the code, simply edit the line
  opts->isFlipY = true; //false: images in raw DICOM orientation, true: image rows flipped to cartesian coordinates
in nii_dicom_batch.cpp to read
 opts->isFlipY = false;
and re-compile. You can likewise edit the orthogonal rotations applied to 3D images.

The COMPILE.md file will provide details if you want to compile on a Windows computer.