Hello, 


Because I had problems finding automatically the corpus callosum
cutting plane, I loaded the wm volume, click in the center of the
corpus in coronal view, switch to sagittal plane and used the volume
RAS coordinates (tailarach coord says "none"). then I ran this line:


recon-all -stage2 -cc-xyz -2.0 25.0 0.0 -subjid 22970


but it showed this:


<color><param>FFFF,0000,0000</param>...

masking possible pons locations using cc cutting plane

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;

brainstem (min, max) thickness = (15,35)

brainstem min height = 25

min_delta_thickness = 6

min_cont_brainstem_thickness = 8

min_cont_brainstem_height = 3

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

area[0] = 78 (min = 350, max = 790), aspect = 0.52 (min = 0.60, max =
1.20)

need search nearby

using +/- offset search region where offset is 3.....

using +/- offset search region where offset is 6.....

using +/- offset search region where offset is 9.....

using +/- offset search region where offset is 12.....

using +/- offset search region where offset is 15.....

using +/- offset search region where offset is 18.....

using +/- offset search region where offset is 21.....

using +/- offset search region where offset is 24.....

using +/- offset search region where offset is 27.....

using +/- offset search region where offset is 30.....

using +/- offset search region where offset is 33.....

using +/- offset search region where offset is 36.....

using +/- offset search region where offset is 39.....

using +/- offset search region where offset is 42.....

using +/- offset search region where offset is 45.....

using +/- offset search region where offset is 48.....

initial attempt at finding brainstem failed - initiating backup plan
A....

brainstem (min, max) thickness = (15,35)

brainstem min height = 25

min_delta_thickness = 6

min_cont_brainstem_thickness = 8

min_cont_brainstem_height = 3

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

area[0] = 78 (min = 350, max = 790), aspect = 0.52 (min = 0.60, max =
1.20)

need search nearby

using +/- offset search region where offset is 3.....

using +/- offset search region where offset is 6.....

using +/- offset search region where offset is 9.....

using +/- offset search region where offset is 12.....

using +/- offset search region where offset is 15.....

using +/- offset search region where offset is 18.....

using +/- offset search region where offset is 21.....

using +/- offset search region where offset is 24.....

using +/- offset search region where offset is 27.....

using +/- offset search region where offset is 30.....

using +/- offset search region where offset is 33.....

using +/- offset search region where offset is 36.....

using +/- offset search region where offset is 39.....

using +/- offset search region where offset is 42.....

using +/- offset search region where offset is 45.....

using +/- offset search region where offset is 48.....

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 +/- offset search region where offset is 3.....

using +/- offset search region where offset is 6.....

using +/- offset search region where offset is 9.....

using +/- offset search region where offset is 12.....

using +/- offset search region where offset is 15.....

using +/- offset search region where offset is 18.....

using +/- offset search region where offset is 21.....

using +/- offset search region where offset is 24.....

using +/- offset search region where offset is 27.....

using +/- offset search region where offset is 30.....

using +/- offset search region where offset is 33.....

using +/- offset search region where offset is 36.....

using +/- offset search region where offset is 39.....

using +/- offset search region where offset is 42.....

using +/- offset search region where offset is 45.....

using +/- offset search region where offset is 48.....

mri_fill: could not find pons

No such file or directory

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.

INFO: Modifying dst c_(r,a,s), using the transform dst

INFO: Modifying dst c_(r,a,s), using the transform dst

talairach cc position changed to (-2.00, 25.00, 0.00)

INFO: Modifying dst c_(r,a,s), using the transform dst

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

ERROR: mri_fill exited with non-zero status

------------------------------------------

Filesystem   512-blocks     Used     Avail Capacity  Mounted on

/dev/disk0s9  320144448 98977240 220655208    31%    /

------------------------------------------

recon-all exited with errors at Wed Jan 26 16:07:52 EST 2005


</color><color><param>0000,0000,0000</param>

what could be the problem?


thanks a lot.


wan</color>