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>> 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> > 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> > 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> > > -- 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
