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 <greve@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
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