> 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 EDT 2010 > /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-Ubuntu SMP Wed May 26 23:35:15 UTC 2010 i686 GNU/Linux > > recon-all exited with ERRORS at Tue Jun 22 08:27:59 EDT 2010 > > 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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