help > RE: Qform matrix in MRIcron and MRIcroGL
Jan 6, 2021  12:01 PM | Chris Rorden
RE: Qform matrix in MRIcron and MRIcroGL
Your data is anisotropi and not aligned with canonical space, hence the 'resliced' seen in the MRIcroGL status bar. Note that MRIcron will also manipulate the header depending on your Preferences (e.g. you can choose if MRIcron loads the raw data as stored on disk, orthogonally losslessly rotates the data to match the canonical NIfTI space, or resamples the data).

Be aware that NIfTI stores two spatial transforms: the quaternion-based QForm (9 DoF) and matrix based SForm (12 DoF). When both are set, both MRIcron and MRIcroGL give precedence to the latter as described here:
For consistency across tools you might want to make sure the SForm and QForm is identical, unless a shear is required to represent your transform.

In future, you may want to consider converting images from DICOM to NIfTI using dcm2niix, which will losslessly reorient 3D acquisitions to match canonical space (e.g. reslice your sagittal data to axial). Likewise, choosing an isotropic image resolution during acquisition may make life easier (in your case increasing the scan time by 20%).

When using different systems that have different conventions for how they store data internally, I would suggest always thinking about the coordinates in world space mm, rather than voxel order as stored on disk.

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loutions Jan 6, 2021
RE: Qform matrix in MRIcron and MRIcroGL
Chris Rorden Jan 6, 2021