PETSurfer provides a set of tools within FreeSurfer for Partical Volume Correction (PVC) and Kinetic Modeling. While these are typically used for PET analysis, the tools can be used in any context where PVC is needed. PVC methods include the Symmetric Geometric Transfer Matrix (SGTM), two-compartment model (also known as the Meltzer Method), three-compartment model (also known as the Muller-Gartner (MG) Method), region-based voxel-wise (RBV). SGTM is used for ROI analysis where as the others are used for voxel-wise analysis. All PVC implementations also accounts for the volume fraction effect. PETSurfer will be released with FreeSurfer version 6.
1. gtmseg --s subject
where "subject" is the name of the FreeSurfer subject when you ran recon-all. This creates several files in the FS folder used to run the PVC methods. This should take about an hour or two.
2. Register your PET image with the anatomical:
mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta
where template.nii.gz is the template image for your PET data. If your PET data only has one frame (eg, an SUV image), then that will be your template. If your PET data has multiple frames (ie, dynamic), then you will need to create the template from the dynamic data. This can be done by extracting a single frame (mri_convert pet.nii.gz --frame frameno template.nii.gz) or averaging all the time frames together (eg, mri_concat pet.nii.gz --mean --o template.nii.gz),