The mri_gtmpvc command will remove volume fraction effects. Look at the PETsurfer page. Run it with --psf 0 and use the muller-gartner output. The output will only be valid for gray matter
On 08/12/2017 10:55 AM, Bruce Fischl wrote: > Hi Shane > > we do have some tools to deal with it like > mri_compute_volume_fractions and mri_compute_volume_intensities, or > maybe Doug's PET stuff. At the very least you should probably regress > thickness out. > > cheers > Bruce > > On Sat, 12 Aug 2017, Shane Schofield wrote: > >> Thank you both. >> >> How can I deal with partial volume in this case? Would it be possible >> to use >> the partial volume tool for PET on my MD volumes? Sorry if it is a silly >> idea. >> >> Best Wishes, >> Shane >> >> >> On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia >> <ayend...@mgh.harvard.edu> wrote: >> >> >> Agreed, especially so with MD. Keep in mind that you¹re upsampling MD >> from >> a lower-res (diffusion) space to a higher-res (T1) space, so it >> should be >> smooth already, relatively to measure derived from the T1. And MD varies >> pretty smoothly (it¹s a mean of 3 things, after all). >> >> On 8/11/17, 1:11 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >> >> >Hi Shane >> > >> >not really - it totally depends on the size of the effect you are >> looking >> >for. I would be *very* careful about partial volume effects though >> > >> >cheers >> >Bruce >> >On Fri, >> >11 Aug 2017, Shane Schofield wrote: >> > >> >> Appreciate it Dr Bruce. Do you have guidelines for smoothing MD? >> >> >> >> Dr Yendiki, I am trying to investigate whether cortical MD can be a >> >>marker >> >> of neurodegeneration. The idea is that during the early stages of a >> >>disease, >> >> cellular microstructure may breakdown before cortical thinning >> occurs. >> >>This >> >> results in "less" barriers against diffusion resulting in an >> increase of >> >> MD. >> >> >> >> >> >> On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl >> >> <fis...@nmr.mgh.harvard.edu> wrote: >> >> >> >> >> >> Hi Shane >> >> >> >> you probably don't need cvs as it is more to extend the surface-based >> >> registration to the entire volume. Here you just need the >> surface-based >> >> registration I believe. Use mri_vol2surf to sample the FA onto the >> >>surface. >> >> After that it is identical to a thickness study >> >> >> >> cheers >> >> Bruce >> >> >> >> >> >> >> >> On Fri, 11 Aug 2017, Shane Schofield >> >> wrote: >> >> >> >> > Thanks Dr Yendiki. >> >> > >> >> > I am more interested to compare MD in grey matter regions by >> putting >> >>the >> >> MD on the surface, and then do a glmfit type of comparisons. Is >> that OK? >> >> Would you recommend me >> >> > to smooth the data after spatial normalisation? I have also used >> the >> >> mri_cvs_register as described on the tutorial. >> >> > >> >> > >> >> > On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield >> >> <shane.schofi...@yahoo.com> wrote: >> >> > >> >> > >> >> > Hi DTI Experts, >> >> > >> >> > Is it sensible to do comparisons of MD on the cortex surface like a >> >>normal >> >> cortical thickness comparisons between group? If the answer is >> yes, are >> >> there recommended on >> >> > smoothing ? >> >> > >> >> > DT_RECON has been completed in Freesurfer. >> >> > >> >> > Thank you. >> >> > >> >> > >> >> > >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> 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. >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > > _______________________________________________ > Freesurfer mailing list > 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 Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
