Dear Freesurfer experts:

My project objective is to build 3D reconstruction of brain with inserted electrodes. I want register the Brian volume of CT and MR via freesurfer. The registration result looks great when I used th "mri_coreg" instruction, but when I tried to use the information in lta data to register by myself, some trouble happens.

The LTA data -------------------------------------------------------------------------------------------------------------------------------------------------------------- # transform file p19_movCT2refMR.lta # created by caca on Tue Jan 24 17:45:08 2017

type = 0 # LINEAR_VOX_TO_VOX nxforms = 1 mean = 0.0000 0.0000 0.0000 sigma = 10000.0000 1 4 4 4.795561134815216e-01 -1.318652089685202e-02 -2.057363465428352e-02 1.383309745788574e+01 1.247252989560366e-02 4.785549342632294e-01 -6.737518310546875e-02 1.315915203094482e+01 1.107159163802862e-02 3.306149691343307e-02 9.974335432052612e-01 -6.133582305908203e+01 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 src volume info valid = 1 # volume info valid filename = patient19CT.nii volume = 512 512 228 voxelsize = 4.873275756835938e-01 4.873275756835938e-01 9.999971985816956e-01 xras = -9.993908405303955e-01 -0.000000000000000e+00 3.489949554204941e-02 yras = -0.000000000000000e+00 1.000000000000000e+00 -0.000000000000000e+00 zras = 3.489949554204941e-02 0.000000000000000e+00 9.993908405303955e-01 cras = 7.397460937500000e-02 -1.105121917724609e+02 1.181088867187500e+02 dst volume info valid = 1 # volume info valid filename = patient19MR.nii volume = 256 256 192 voxelsize = 1.015599966049194e+00 1.015599966049194e+00 1.000001072883606e+00 xras = -1.000000000000000e+00 -0.000000000000000e+00 0.000000000000000e+00 yras = -0.000000000000000e+00 1.000000000000000e+00 -0.000000000000000e+00 zras = -0.000000000000000e+00 -0.000000000000000e+00 1.000000000000000e+00 cras = 3.934204101562500e+00 2.904579925537109e+01 1.511990356445312e+01 subject unknown -------------------------------------------------------------------------------------------------------------------------------------------------------------------

First I thought the 4x4 matrix is the affine matrix (type = VOX_TO_VOX)

4.795561134815216e-01 -1.318652089685202e-02 -2.057363465428352e-02 1.383309745788574e+01 1.247252989560366e-02 4.785549342632294e-01 -6.737518310546875e-02 1.315915203094482e+01 1.107159163802862e-02 3.306149691343307e-02 9.974335432052612e-01 -6.133582305908203e+01 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00

After I studied the document "FS Coordinates (PDF)" at the following URL : http://freesurfer.net/fswiki/CoordinateSystems there are some question :

I thought in my case correspond to the page 3 condition "Two Fields of View, Two Coordinate Systems" But I am not sure that that does the affine matrix above is the vox_to_vox matrix or not. If it is, could I use it directly to compute the corresponding voxel location between 2 volume? or I need additional coordinate transfer?

Sincerely, Hsintsung