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.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 > > > > > > _______________________________________________ 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. 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