Hi Jeff,
I see this relatively often. Eventhough the talairach registration is fine, the ICV is underestimated. In this case I take old ICV, which helps.
mri_segstats --subject $MYSUBJECT --old-etiv-only
This is in 99% of these cases a cure. This is not just a blind attempt. In these cases I then compare each ICV normalized aseg volume against an age matched group and only if the old-etiv-only ICV gives better estimates I use it.
Cheers,
Martin
On Thursday 25 February 2010 23:05:10 Jeff Sadino wrote:
Thanks Doug. That is very good news to hear!
Maybe I spoke too soon about fixing the problem. I looked at 4 more subjects, and even though the icv value is unique, its magnitude seems wrong. Often times, it is smaller than the BrainSegVol, which doesn't make much sense and it is also low overall.
# subjectname 090167_F01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1639959, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1639959.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1289194.000000, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1299686, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1299686.000000, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1105595.114652, mm^3
# subjectname 090182_S01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1599981, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1599981.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1199694.000000, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1205382, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1205382.000000, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1114008.197334, mm^3
# subjectname 090187_F01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1826694, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1826694.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1381871.000000, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1388801, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1388801.000000, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1307759.303915, mm^3
# subjectname 100014_F01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1948121, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1948121.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1467582.000000, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1488088, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1488088.000000, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1637915.031593, mm^3
# subjectname 040002_S04_test # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1774481, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1774481.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1288022.000000, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1312132, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1312132.000000, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1302696.178406, mm^3
I had also done 040002_S04 in fs 3.0.5, and this is the result: # subjectname 040002_S04 # BrainMaskFile mri/brainmask.mgz # BrainMaskFileTimeStamp 2008/29/08 15:44:46 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1753272, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1753272.000000, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1310474, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1310474.000000, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1767481.547316, mm^3
All of the values are similar except the icv. Do you guys have any ideas where I can look for the answer?
Thank you very much, Jeff