this is probably the problem(from log below):

using +/- offset search region where offset is 48..... mri_fill: could not find pons No such file or directory

you need to define the pons as well.

you may want to first try to get a good talairach transform. have you run: talairach 22970

then check to see if it is correct: tkmedit 22970 orig -main-transform talairach.xfm

if it looks good, then stage2 should finish without errors. if not, you may want to try talairach_mgh, or copy the talairach script somewhere and modify it to use the brain volume as input. that will often improve the talairach. also make sure the COR-.info file in mri/wm has a line beginning: xform

followed by the path to the talairach.xfm file ($SUBJECTS_DIR/22970/mri/transforms/talairach.xfm)

if you have a good talairach transforms and stage2 finishes with errors, page ~32 in the FS guide should show where to select the CC and pons points. if you don't have talairach coords or you just can't seem to get a good transform for you data, then use the RAS(but remove the talairach.xfm file and xform line in COR-.info).

-- brian t. quinn

On Wed, 26 Jan 2005, Wan Park wrote:

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:

... 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

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Filesystem 512-blocks Used Avail Capacity Mounted on /dev/disk0s9 320144448 98977240 220655208 31% /

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

what could be the problem?

thanks a lot.

wan