Actually, I think it only will affect the volume measurement for each
structure, so that's no good. There is not a flag to mri_segstats that
will do this. If you have a registration between your native pet data
and the FS anat, then you can use
mri_compute_volume_fractions regfile.dat pet.nii pvf
This will create pvf.{gm,wm,csf}.mgz
You can then correct the pet with something like
fscalc pet.nii div pvf.gm.mgz pet.pvf.nii
You can map the aparc+aseg into the pet space using mri_label2vol (and
the reg from above), then use mri_segstats with the files in the native
pet space.
doug
corinna bauer wrote:
> Hi Doug,
> I will give that a try. How will this account for the p.v. in pet
> data? Does it remove the voxels that are mixed tissue classes? Does it
> account for partial volume effects between neighbouring grey matter
> structures?
> Corinna
>
> On Wed, Jun 8, 2011 at 1:06 PM, Douglas N Greve
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Corinna,
> try adding --pv mri/norm.mgz
> doug
>
> corinna bauer wrote:
>
> Hi all,
> I am wondering if partial volume is taken into account when
> calculating average uptake values of pet data. I know that
> aseg.stats takes partial volume into account and I am
> wondering if there is something similar in place for pet data?
> From what I gather, most people when using FreeSurfer correct
> for partial volume effects by regressing out cortical
> thickness, but no basis for this correction method has been
> provided. Any insight would be appreciated.
>
> n.b. to obtain the pet uptake values I used mri_segstats --seg
> mri/aparc+aseg.mgz --sum pet.segstats.dat --i $petanat --ctab
> rois.txt
>
> Thank you,
> Corinna
>
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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