Did you check the transform to make sure it is accurate? tkregister2 --s subject --fstal --surf
It could be that the scaling is not good. I've seen this before (no solution yet). doug 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 > > On Thu, Feb 25, 2010 at 11:14 AM, Jeff Sadino > <jsadino.que...@gmail.com <mailto:jsadino.que...@gmail.com>> wrote: > > Doug - > Thank you for your suggestion. I looked, and the > talairach_with_skull.lta file was unique to each subject. > However, the talairach.xfm file was actually a shortcut to > /apps/freesurfer3/subjects/fsaverage/mri/transforms/talairach.xfm. > This is because of some in-house legacy code that we use to do > some preprocessing. After fixing this, the icv value came out unique. > > Too bad it is in the beginning of the reconstruction stream. 149 > subjects is going to take a while to redo. Besides the icv > measurements, will this file effect other outputs, or could I just > rerun the segstats command? > > Nick - > Sorry, I should have been more clear. I reran them in fs4 from > scratch, using a different subject directory, so the two recons > should hopefully be completely independent of each other. > > Thanks Everyone! > Jeff > > > On Fri, Feb 19, 2010 at 12:47 PM, Nick Schmansky > <ni...@nmr.mgh.harvard.edu <mailto:ni...@nmr.mgh.harvard.edu>> wrote: > > also note that if the subjects were processed by a prior > version, then > when re-run with v4.X, talairach.xfm will not get overwritten, > as it is > assuming it was edited. so you should check of talairach.xfm and > talairach.auto.xfm are the same, and if not either re-run with > -clean-tal, or just copy talairach.auto.xfm to talairach.xfm. > > n. > > > On Fri, 2010-02-19 at 17:41 -0500, Douglas N Greve wrote: > > Can you check the talairach.xfm and the > talairach_with_skull.lta to make > > sure that they are different across subject? > > > > Jeff Sadino wrote: > > > Hi Doug, > > > > > > Thanks for the quick reply. It just seems like an error > that all 149 > > > subjects would line up exactly with the talairach > transform (that > > > would give a determinant of 1.000000?). > > > > > > The following commands I used from my script were: > > > recon-all -sd /scratch/data431 -s 040002_S04 -autorecon1 > > > *code to check for errors* > > > recon-all -sd /scratch/data431 -s 040002_S04 -autorecon2 > > > *code to check for errors* > > > recon-all -sd /scratch/data431 -s 040002_S04 -autorecon3 > > > *code to check for errors* > > > > > > I searched the recon-all log for "-notalairach" and came > up with no > > > hits. Any other ideas? > > > > > > I ran all of these subjects in fs3 a while ago using an > older version > > > of my script, and they all came out with unique icv values. > > > > > > Thank you again for your suggestions! > > > Jeff Sadino > > > > > > On Fri, Feb 19, 2010 at 12:04 PM, Douglas N Greve > > > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > > > > The ICV is *estimated* from the talairach transform. > Did you > > > happen to run recon-all with -notalairach? You can > check that the > > > talairach transforms are all different. > > > > > > doug > > > > > > Jeff Sadino wrote: > > > > > > Hello, > > > I reconed 149 subjects using freesurfer 4.3.1 > automatically > > > using our cluster. When I did asegstats2table, > all 149 > > > subjects had the exact same icv: > > > # Measure IntraCranialVol, ICV, Intracranial Volume, > > > 1948106.000000, mm^3 > > > > > > Running mri_segstats manually, here is the > beginning of the > > > output: > > > > > > mri_segstats --seg mri/aseg.mgz --sum > stats/aseg2.stats --pv > > > mri/norm.mgz --excludeid 0 --brain-vol-from-seg > --brainmask > > > mri/brainmask.mgz --in mri/norm.mgz > --in-intensity-name norm > > > --in-intensity-units MR --etiv --surf-wm-vol --ctab > > > $FREESURFER_HOME/ASegStatsLUT.txt --subject 040002_S04 > > > atlas_icv (eTIV) = 1948106 mm^3 (det: 1.000000 ) > > > Loading mri/aseg.mgz > > > Getting Cerebral WM volumes from surface > > > lh white matter volume 246101 > > > rh white matter volume 251160 > > > Loading mri/norm.mgz > > > Loading mri/norm.mgz > > > Loading mri/brainmask.mgz > > > # nbrainmaskvoxels 1766623 > > > # brainmaskvolume 1766623.0 > > > # nbrainsegvoxels 1310448 > > > # brainsegvolume 1310448.0 > > > Voxel Volume is 1 mm^3 > > > Generating list of segmentation ids > > > Found 50 segmentations > > > Computing statistics for each segmentation > > > 1 2 Left-Cerebral-White-Matter 247216 247216 > > > > > > Looking at the log files for several other > subjects, they all > > > have a determinant of 1. However, all of the > other numbers - > > > brainmask, brain seg volume, individual regions - > are all > > > unique and correct. It is just the icv. Can > anyone point me > > > in the right direction of how to investigate the > determinant > > > value? > > > > > > Here is the mri_segstats version: # cvs_version $Id: > > > mri_segstats.c,v 1.33.2.5 2009/02/11 22:38:51 > nicks Exp $ > > > > > > Thanks! > > > Jeff Sadino > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > > Phone Number: 617-724-2358 Fax: 617-726-7422 > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > -- 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
