Hi Doug, I used the mri_compute_volume_fractions and fscalc commands and got this error message:
mri_compute_volume_fractions: Command not found. fscalc: Command not found. Other FreeSurfer commands, such as mri_segstats are working fine in the same batch script. Corinna On Wed, Jun 8, 2011 at 2:30 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > > > 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 > >
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