questions > RE: dcm2niix options
Sep 3, 2017  10:09 PM | Chris Rorden
RE: dcm2niix options
  The latest versions of dcm2niix are more sophisticated. It will rotate 3D acquisitions to the nearest orthogonal to a NIfTI identity matrix. If you request the crop ('-x y') than you should get both the original as well as a cropped scan.

In addition, tools like BET have become better - for T1 scans I have been impressed by the "Robust" (-R) option.

Finally, for my own data I use SPM to compute how to align the T1 scan to standard space and then impose a bounding box. Crucially, like dcm2niix this cropping is done losslessly for the surviving voxels: the data is not resampled.

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Keith Schneider Nov 25, 2015
Chris Rorden Nov 30, 2015
Jason Craggs Sep 3, 2017
RE: dcm2niix options
Chris Rorden Sep 3, 2017