Hello Nathan,
If you want stats related to the ?h.cortex.label (e.g., average cortical
thickness) you can do the following:
mris_anatomical_stats -l {$hemi}h.cortex.label -f
$id/stats/{$hemi}h.cortex.stats $id {$hemi}h
The resulting ?h.cortex.stats file will contain all the same
measures (e.g., NumVert, SurfArea, GrayVol, ThickAvg, etc) as ?
h.aparc.stats, but the values will be specific to (overall) cortex
(as defined by ?h.cortex.label).
And you can even use 'aparcstats2table' to collect these values if you
wish.
e.g.,
aparcstats2table --subjects subj1 <subj2 ...> --h lh --parc cortex --
meas thickness --t avgCortexThickness.txt
cheers,
Mike H.
On Wed, 2009-03-11 at 18:25 -0400, Douglas N Greve wrote:
> Actually, I don't think we do. ?h.aparc.stats has total cortical area
> and aseg.stats has surface-based white matter volume. You can get it
> with something like:
>
> mri_segstats --slabel subject lh
> $SUBJECTS_DIR/subject/label/lh.cortex.label --sum lh.cortex.stats --i
> $SUBJECTS_DIR/subject//lh.volume
>
> Then multiply the "Mean" by the number of vertices.
>
> We'll have to add a better method to mris_anatomical_stats.
>
> Bruce Fischl wrote:
> > Hi Nathan,
> >
> > I think we do output the total cortical volume in one of the stats
> > files,but I don't remember where it is. Doug, Nick or Krish: do any of
> > you know?
> >
> > Bruce
> >
> > On Wed, 11 Mar 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
> >
> >> Bruce,
> >>
> >> In that case, is there a way to have freesurfer output average cortical
> > thickness throughout the entire cortex? In terms of total volumes, I
> > noticed measures labeled IntraCranialVol and BrainSegVol in the wmparc
> > and aseg stats files. I assume intracranial volume includes
> > everything, even non-cortical regions? If that is so, is BrainSegVol
> > a measure of total cortical volume? I also noticed that the values in
> > BrainSegVol differ greatly between the two stats files. Your help is
> > greatly appreciated,
> >
> >>
> >> Nathan
> >>
> >>
> >> -----Original Message-----
> >> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> >> Sent: Wed 3/11/2009 12:47 PM
> >> To: Dankner, Nathan (NIH/NIMH) [F]
> >> Cc: freesurfer@nmr.mgh.harvard.edu
> >> Subject: Re: [Freesurfer] Aparcstats question
> >>
> >> Hi Nathan,
> >>
> >> the "unknown" label is intended to be non-cortical regions such as the
> >> callosum, and should be ignord. I think total white matter volume is
> >> generated by default, but maybe Nick or Doug can correct me (although
> >> Nick
> >> is out of the country)
> >>
> >> Bruce
> >>
> >>
> >> On Wed, 11 Mar 2009, Dankner, Nathan
> >> (NIH/NIMH) [F] wrote:
> >>
> >>> Hello all, I sent this a couple of weeks ago but it must have
> >>> slipped through the cracks:
> >>>
> >>> I have a couple of questions regarding the stats files. First, at the
> >>> beginning of the aparc.stats tables, there is a measure that is labeled
> >>> ³unknown.² Is this total average thickness throughout the cortex,
> >>> or just
> >>> some throw-away measure?
> >>>
> >>> Secondly, I have heard that there are command line flags that can be
> >>> used to
> >>> find things such as total white matter volume, etc. What are these
> >>> flags?
> >>> Thank you in advance,
> >>>
> >>> Nathan
> >>>
> >>>
> >>
> >>
> >>
> >>
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