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.que...@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 > <gr...@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.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.
