Re: [Freesurfer] pet partial volume correction

corinna bauer wrote:

Alright that should work. So do I use the pet.anat.nii files (from mri_vol2vol) as the input pet file to the mri_compute_volume_fractions?

No, use the pet volume. This does everything in the pet space.

Also, has anyone published using this pv correction method that you know of?

I don't know. I think this is how they do pvc in pet, but I really don't know the lit.

An alternative method that I was thinking was to do something similar to the cortical thickness correction Salat used and sample on either side of the gray/white boundary and the gray/csf boundary and calculate the ratio. Do you think this could account for the effects of pv in pet?

David's method was not for doing pvc, and I would not use it for pet.

doug

Corinna

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