On Wed, Jun 8, 2011 at 1:44 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

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 <greve@nmr.mgh.harvard.edu <mailto:greve@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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