Hi Joan,
I don't think we've ever seen that happen. Did the skull stripping fail? What version are you running? Can you send us an image of the aseg.mgz?
Bruce
On Sun, 25 Mar 2007, Joan Fisher wrote:
Hi all -- I've had problems recently with the subcortical segmentation, where it calls the caudate the hippocampus and the putamen is labeled the amygdala, etc. I'm wondering if the WM/GM volumes can still be accurate (which it looks like based on wm.mgz) when the identification of these structures is so far off.
Also, the aseg.stats file was generated but contains no data, even though autorecon2 and 3 completed with no reported errors. What can I do to get the aseg.stats information? Running it again didn't fix the problem.
Please let me know if there's an alternate way to get the WM and GM volumes for each hemisphere, even if the aseg.stats isn't working.
Many thanks, Joan Fisher
This is what aseg.stats looks like:
# Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.11.2.5 2006/04/13 18:57:07 nicks Exp $ # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject 007 # sysname Darwin # hostname joan-fishers-powerbook58.local # machine Power Macintosh # user joanfisher # anatomy_type volume # # SUBJECTS_DIR /Users/joanfisher/subjects # subjectname 007 # BrainMaskFile mri/brainmask.mgz # BrainMaskFileTimeStamp 2007/19/02 18:02:57 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1447820, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1447820.000000, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1158492, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1158492.000000, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1105720.605166, mm^3 # SegVolFile mri/aseg.mgz # SegVolFileTimeStamp 2007/24/02 08:19:55 # ColorTable /Applications/freesurfer/FreeSurferColorLUT.txt # ColorTableTimeStamp 2007/14/00 12:14:41 # InVolFile mri/norm.mgz # InVolFileTimeStamp 2007/23/02 14:29:21 # InVolFrame 0 # PVVolFile mri/norm.mgz # PVVolFileTimeStamp 2007/23/02 14:29:21 # ExcludeSegId 0 # VoxelVolume_mm3 1 # TableCol 1 ColHeader Index # TableCol 1 FieldName Index # TableCol 1 Units NA # TableCol 2 ColHeader SegId # TableCol 2 FieldName Segmentation Id # TableCol 2 Units NA # TableCol 3 ColHeader NVoxels # TableCol 3 FieldName Number of Voxels # TableCol 3 Units unitless # TableCol 4 ColHeader Volume_mm3 # TableCol 4 FieldName Volume # TableCol 4 Units mm^3 # TableCol 5 ColHeader StructName # TableCol 5 FieldName Structure Name # TableCol 5 Units NA # TableCol 6 ColHeader normMean # TableCol 6 FieldName Intensity normMean # TableCol 6 Units MR # TableCol 7 ColHeader normStdDev # TableCol 7 FieldName Itensity normStdDev # TableCol 7 Units MR # TableCol 8 ColHeader normMin # TableCol 8 FieldName Intensity normMin # TableCol 8 Units MR # TableCol 9 ColHeader normMax # TableCol 9 FieldName Intensity normMax # TableCol 9 Units MR # TableCol 10 ColHeader normRange # TableCol 10 FieldName Intensity normRange # TableCol 10 Units MR # NRows 1 # NTableCols 10 # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 666 -1414545516 -0.0
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