Hi All,
I am trying to understand the handling of transforms and strides in mrtrix and stumbled upon the following situation.
I have an image that has the following raw header information (mrinfo -norealign) :
Dimensions: 82 x 82 x 46
Voxel size: 2.70732 x 2.70732 x 2.7
Data strides: [ 1 2 3 ]
Format: NIfTI-1.1 (GZip compressed)
Data type: 32 bit float (little endian)
Intensity scaling: offset = 0, multiplier = 1
Transform: -0.9938 0.1115 0 100.8
0.1115 0.9938 0 -96.89
0 0 1 -29.52
comments: FSL5.0
Which MRtrix prefers to massage into (mrinfo):
Dimensions: 82 x 82 x 46
Voxel size: 2.70732 x 2.70732 x 2.7
Data strides: [ -1 2 3 ]
Format: NIfTI-1.1 (GZip compressed)
Data type: 32 bit float (little endian)
Intensity scaling: offset = 0, multiplier = 1
Transform: 0.9938 0.1115 0 -117.1
-0.1115 0.9938 0 -72.44
-0 0 1 -29.52
comments: FSL5.0
Now, when I use mrview to visualize this image using both commands mrview image.nii and mrview image.nii -norealign. I get the exact same visualization. Intuitively, I would have expected one to show up in RAS and the other in LAS. As well as, voxel [0, 0,0] to be at -117,-72,-29 in one case and at 100,-96,-29 in the other case.
It’s likely I am still confused about how the images are being displayed.
Any suggestions?
Thanks!
Emilie