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?
Also, has anyone published using this pv correction method that you know of?
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?
Corinna
On Wed, Jun 8, 2011 at 1:44 PM, Douglas N Greve
<gr...@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 <
>> 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
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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