Thank you Martin and Nick for the clarification about how to verify the talairach transformation in the newer FreeSurfers. I think I am going to use the -use-mritotal command, as this was giving more reasonable ICVs around 1.3L - 1.7L. I am still manually checking the outliers. According to the ICV measurement, this one seems way off, but I'm not sure how to judge the severity of the transform. On a scale of 1 to 10, 1 being bad, how would this one rate? How much would this cause the ICV to be off?
Thank you, Jeff
On Mon, Jan 30, 2012 at 8:47 AM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
Jeff,
to check the tal reg, use:
tkregister2 --s subjid --fstal --surfs
i've corrected the eTIV page to reflect this. --fstal loads mni305 as the target. the target used in the tal reg step (711-2C...) is registered with the mni305. note that --surfs is optional, as the surfaces may not exist yet.
Nick
On Fri, 2012-01-27 at 18:53 -0500, Martin Reuter wrote:
Hi Jeff,
I am not sure about which atlas, but concerning the transforms:
4.2 and earlier: talairach_with_skull.lta later versions: talairach.xfm
I am pretty convinced that the way to check as described here http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV
cd $SUBJECTS_DIR/subject/mri/transforms tkregister2 --xfm talairach.xfm \ --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca \ --mov ../nu_noneck.mgz --reg junk
is correct in newer FS versions, but maybe double check with Nick.
Best, Martin
On Fri, 2012-01-27 at 13:39 -1000, Jeff Sadino wrote:
bump :)
any feedback on this would be very much appreciated. Thank you!
Jeff
On Mon, Jan 23, 2012 at 6:56 PM, Jeff Sadino jsadino.queens@gmail.com
wrote:
Hello,
Thank you Nick, Martin, and Doug for your previous feedback about
ICV.
I have a couple more questions that I am hoping you could clarify
for
me.
To verify my ICV value, some pages on the mailing list and wiki say
to
use this command: tkregister2 --s subject --fstal --surf
Other places say to use this: tkregister2 --xfm talairach.xfm --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca --mov ../nu_noneck.mgz --reg junk
However, on this wiki page (http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV), it says that post fs4.2.0, the template is this file: 711-2C_as_mni_average_305.4dfp.img. In the first tkregister2 command above, doesn't the --fstal flag use the talairach template? But shouldn't it be using the 711 template? And since I am using
fs5.0.0,
does that mean that I should not be using the RB template? Ultimately, what is the correct way to verify the ICV in fs 5.0.0?
Thank you very much, Jeff Sadino
On Mon, Mar 1, 2010 at 7:57 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
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 >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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