Hi Lena,
-notal-check will disable the error detection, not the tal itself, so
won't help in cases where the xform is truly wrong. The image you sent
looks PD/T2* weighted, which won't work for the talairaching we use (or for
many of our analysis steps).Do you have a T1-weighted image?
cheers
Bruce
On Thu, 8 Jul 2010, Lena
Palaniyappan wrote:
The original image is attached -
Even after notal-check, the recon exits with error
mri_watershed Error:
GLOBAL region of the brain empty !
\ (we have not included cerebellum fully in the slices: is this a problem?)
Thanks for your help
On 08/07/2010 16:05, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
well that certainly looks wrong. What does the original image look like?
On
Thu, 8 Jul 2010, Lena Palaniyappan wrote:
I am trying to reconstruct some 7T images but they repeatedly fail Talairach
step
The tkmedit displays normal coronal, sagittal positions for the target.
If I use tkregister2 the moveable appears odd please see the attached
The error message is
#...@# Talairach Failure Detection Thu Jul 8 10:58:38 BST 2010
/Applications/freesurfer/subjects/7TMRIData/szanat05a/mri
\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
The talairach.xfm shows
MNI Transform File
% tkregister2
Transform_Type = Linear;
Linear_Transform =
2.49591112 0.47519815 2.82347846 13.68270206
-3.58282375 2.34796309 -2.66250205 -5.44943428
-2.31779170 -0.83566302 0.94148278 7.01633883 ;
What should I do next?
Thanks
Lena
_______________________________________________________
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of
Nottingham)
South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
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South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
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