RV: FREESURFER - Freesurfer

7 Jul 2010

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Good morning,I am working on brain segmentation using freesurfer
program.
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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.
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The error I get is as follows:
ERROR
               cp transforms/talairach.auto.xfm
transforms/talairach.xfm
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           #--------------------------------------------
           #@#
           Talairach Failure Detection Tue Jun 22 04:45:20 EDT

2010
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           /usr/local/freesurfer/subjects/ome/mri

            talairach_afd -T 0.005 -xfm transforms/talairach.xfm

           ERROR: talairach_afd: Talairach Transform:

transforms/talairach.xfm ***FAILED***
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           (p=0.0063, pval=0.0000 < threshold=0.0050)

I have tested the segmentation with another patient and gives me the
following error.
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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
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           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
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          recon-all exited with ERRORS at Tue Jun 22 08:27:59 EDT

2010
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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.
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Thank you very much. A greeting.
Attentively