On 9/18/2020 12:12 PM, Billah, Tashrif wrote:

Hi there,

How is the rightmost column in `mri_convert -c` calculated?

I have the following fslhd (relevant fields shown only) in a NIFTI image:

dim1            208
dim2            300
dim3            320
qto_xyz:1       0.799690    0.022176   0.001352 -86.687996
qto_xyz:2       -0.021442   0.783122   -0.162051 -62.728546
qto_xyz:3       -0.005816   0.161952   0.783414 -174.620270
qto_xyz:4       0.000000    0.000000   0.000000    1.000000

That looks like it is the qform matrix in the nifti file

After `mri_convert -c`, mri_convert reports the following (relevant fields shown only) in the MGZ image:

voxel to ras transform:
               -1.0000  -0.0000   0.0000   128.0225
               -0.0000   0.0000   1.0000  -101.4184
                0.0000  -1.0000  -0.0000   102.4140
                0.0000   0.0000   0.0000     1.0000

Shouldn't the right-most column be:

                    128.5

                    -128.5

                    128.5
                    1

The numbers are (256+1)/2=128.5

Not necessarily. That matrix still converts from col-row-slice to scanner RAS (or whaterver the qform space is)

Best, Tashrif

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