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