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 > <gr...@nmr.mgh.harvard.edu <mailto: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> > <mailto: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 > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 > gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > <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. > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@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> > > -- 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 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
