Hi Santiago,
if the talairach is correct (you can verify this in tkmedit or tkregister2) then you can just turn the auto checking of the tal transform off in recon-all.
cheers Bruce On Wed, 7 Jul 2010, SANTIAGO GONZALEZ CALERO wrote:
Good morning,I am working on brain segmentation using freesurfer
program.
I wonder if it is possible to turn an initial image with some tool
freesurfer. Because my problem is that when I start to perform segmentation in freesurfer, I get an error and I think that is because dicom image format is a little crooked. If you can not rotate with tkmedit or similar tool.
The error I get is as follows:
ERROR cp transforms/talairach.auto.xfm
transforms/talairach.xfm
#-------------------------------------------- #@# Talairach Failure Detection Tue Jun 22 04:45:20 EDT2010
/usr/local/freesurfer/subjects/ome/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform:transforms/talairach.xfm ***FAILED***
(p=0.0063, pval=0.0000 < threshold=0.0050)I have tested the segmentation with another patient and gives me the
following error.
ERROR
********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...44 iterations mghRead: encountered error executing: 'zcat/usr/local/freesurfer/subjects/francia/mri/T1.mgz',frame -1, errno 12
mri_strip_skull: done peeling brain Brain Size = 1260141 voxels, voxel volume = 1.000 mm3 = 1260141 mmm3 = 1260.141 cm3 mri_watershed Error: read failed Linux freesurfer-virtual 2.6.28-19-generic #61-UbuntuSMP Wed May 26 23:35:15 UTC 2010 i686 GNU/Linux
recon-all exited with ERRORS at Tue Jun 22 08:27:59 EDT2010
Do not know if these errors can be solved with some kind of tool or if
on the contrary are due to initial images of patients are slightly slanted, and if the same could reorient vertically.
Thank you very much. A greeting. Attentively
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