Hi,

I am making ROIs using fslmaths -roi, which requires voxel numbers in the voxel coordinate space. To obtain voxel numbers, I opened MNI_152_2mm_brain from FSL in MRIcroGL and entered the MNI coordinates. It was not straightforward to find voxel coordinates. For example, for MNI coordinates (32, -56, -10), I see these coordinates along with what I assumed to be voxel cordinates (61,35,31), displayed on the title bar. I also tried with fsleyes and got (29, 34, 31) as voxel coordinates. As expected, when I build the ROI with the MRIcroGL voxel coordinates, the ROI is L-R flipped. Is this just some difference in the voxel coordinate systems of FSL and MRIcroGL? Or is there some MRIcroGL config I should know about? And, is there some way to find voxel coordinates from MRIcroGL besides looking at the title bar?

Thanks,

Radha

Radha

I suspect the issue here is that your image has a positive determinant. Some FSL tools (e.g. fslmaths and FSLeyes) mirror the first dimension if the volume has a positive determinant, while other FSL tools (e.g. fslstats) do not. If your spatial transform is not orthogonal with world space, this can also lead to voxel coordinates in other dimensions changing. MRIcroGL returns the i,j,k dimensions as stored on disk.

Both MRIcroGL and FSLeyes will show a left sided ROI on the left side of the axial and coronal images if the viewer is in Neurological convention, and the right side for Radiological convention. You can use the MRIcroGL Preferences window to set up your preferred convention.

You can specify a voxel coordinate (in mm) using the "Coordinates" widgets in the "2D Slice Selection" Panel. Note that the L/R A/P and S/I buttons jump one voxel in the specified direction, and jump to the voxel center to minimize rounding errors. You can also use a Python script to set the location. MRIcroGL always places coordinates in the title bar.