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
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
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 <greve@nmr.mgh.harvard.edu mailto: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 ------------------------------------------------------------------------ _______________________________________________ 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 greve@nmr.mgh.harvard.edu <mailto:greve@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>
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 <greve@nmr.mgh.harvard.edu mailto: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 ------------------------------------------------------------------------ _______________________________________________ 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 greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@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
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 nicks@nmr.mgh.harvard.eduwrote:
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 <greve@nmr.mgh.harvard.edu mailto: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
_______________________________________________ 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 greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@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
You just need to re-run segstats
doug
Jeff Sadino 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 <nicks@nmr.mgh.harvard.edu mailto:nicks@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 > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto: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 > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 > greve@nmr.mgh.harvard.edu <mailto:greve@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 > >
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.queens@gmail.comwrote:
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 < nicks@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 <greve@nmr.mgh.harvard.edu mailto: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
_______________________________________________ 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 greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@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
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.queens@gmail.com mailto:jsadino.queens@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 <nicks@nmr.mgh.harvard.edu <mailto:nicks@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 > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto: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 > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 > greve@nmr.mgh.harvard.edu <mailto:greve@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 > >
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
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.kavec@gmail.comwrote:
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
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.kavec@gmail.com mailto:martin.kavec@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 >
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Jeff Sadino -
Martin Kavec -
Nick Schmansky