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
> > >>
> > >> 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
> >
> >
>
>
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