Re: [Freesurfer] ICV Error fs 4.3.1

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.kavec@gmail.com mailto:martin.kavec@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
>