Hello,

I am trying to generate an inflated surface for a macaque brain, but mri_fill has stopped working for this subject. Below is my command line and output. I specify the corpus callosum and pons as well. Any suggestions?

 

 

mri_fill -CV 101 100 66 -PV 115 140 77 ./mri/wm/wm.nii.gz ./mri/filled/filled.mgz

using voxel position (101, 100, 66) as corpus callosum seed point

using voxel position (115, 140, 77) as pons seed point

reading input volume...done.

searching for cutting planes...INFO: volume does not have linear_transform set nor lta is given by option.-xform.

INFO: use identity matrix as the talairach transform.

INFO: use src volume parameters for the talairach volume.

voxel to talairach voxel transform

1.000   0.000   0.000   0.000;

0.000   1.000   0.000   0.000;

0.000   0.000   1.000   0.000;

0.000   0.000   0.000   1.000;

Calculated talairach cc position (-8.26, -12.19, 56.63)

Using the seed to calculate the cutting plane

find_cutting_plane:seed point not in structure! Searching neighborhood...

Looking for area (min, max) = (350, 1400)

area[0] = 1 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75)

need search nearby

using seed (101, 100, 66), TAL = (-8.3, -12.2, 56.6)

talairach voxel to voxel transform

1.000   0.000   0.000   0.000;

0.000   1.000   0.000   0.000;

0.000   0.000   1.000   0.000;

0.000   0.000   0.000   1.000;

talairach cc position changed to (-8.26, -12.19, 56.63)

Using voxel pons seed point, calculated talairach pons position (5.74, -1.19, 16.63)

find_cutting_plane:seed point not in structure! Searching neighborhood...

Looking for area (min, max) = (350, 790)

area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20)

need search nearby

using seed (115, 140, 77), TAL = (5.7, -1.2, 16.6)

talairach voxel to voxel transform

1.000   0.000   0.000   0.000;

0.000   1.000   0.000   0.000;

0.000   0.000   1.000   0.000;

0.000   0.000   0.000   1.000;

done.

seed_search_size = 9, min_neighbors = 5

search rh wm seed point around talairach space:(9.74, -12.19, 56.63) SRC: (119.00, 100.00, 66.00)

could not find rh seed point around (119, 100, 66)