It's hard to tell from the coronal, but it looks ok. The problem is more visible in the sagittal.
doug Jeff Sadino wrote: > Hello Doug, > > I loaded up the tkregister2 program and I think I see some poor > transformations. I've never really used it before though. Am I just > looking at whether or not the green line lines up with the target > image wm? Can you look at my pictures real quick? 040002_S04_test is > from fs4 that is having problems. 040002_S04 is from fs3 and has a > good icv value. Some of the blank spots are from my graphics drivers > and unrelated to fs. tkregister2 also said the determinant of > 040002_S04_test was 1.49544. > > Martin, > > Thank you for the idea. I did this, and got a much better icv. On > fs3, where the icv was good, the number was 1,767,481. On fs4, it was > 1,302,696. Using your idea on fs4, it was 1,819,485. > > Thank you so much to everyone for your help! > Jeff > > On Thu, Feb 25, 2010 at 8:53 PM, Martin Kavec <martin.ka...@gmail.com > <mailto:martin.ka...@gmail.com>> wrote: > > 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 > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
