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Hello FreeSurfer Developers, I am trying to reconstructing surface of monkey brain. I have got surface files, such as ?h.white, ?h.pial, ?h.area and so on. However, I found the surface light was abnormally dark(as shown in following picture), it seems like that the light source was inside the brain. And I found the RAS and SurfaceRAS coordiantes were different. I got the surface files as following steps: (1) I got the wm.mgz file manually; (2) I filled the wm.mgz and changed the values in left and right hemispheres to 255 and 127, respectively; (3) I generated ?h.orig via command "mri_tessellate filled.mgz 255 lh.orig -n" Then I found RAS and SurfaceRAS coordiantes in ?h.orig were different.

Which steps did I made a mistake? The voxel size of raw image was 0.5*0.5*0.5 mm, was the image resolution the cause?

Thank you very much!

zhiwei

here is the information of raw image: Volume information for T1.mgz type: MGH dimensions: 137 x 175 x 107 voxel sizes: 0.500000, 0.500000, 0.500000 type: FLOAT (3) fov: 87.500 dof: 0 xstart: -34.2, xend: 34.2 ystart: -43.8, yend: 43.8 zstart: -26.8, zend: 26.8 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -6.0000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 3.7500

talairach xfm : Orientation : RAS Primary Slice Direction: axial

voxel to ras transform: 0.5000 0.0000 0.0000 -33.7500 0.0000 0.5000 0.0000 -49.7500 0.0000 0.0000 0.5000 -23.0000 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant 0.125

ras to voxel transform: 2.0000 0.0000 0.0000 67.5000 0.0000 2.0000 0.0000 99.5000 0.0000 0.0000 2.0000 46.0000 0.0000 0.0000 0.0000 1.0000