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 ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.