You will need to run gtmseg --s subject (takes an hour or so), then add --seg gtmseg.mgz to the cmd line
On 08/14/2017 04:12 PM, Shane Schofield wrote: > Hi Dr Greve, > > Are the settings correct to do partial volume correction of my MD images? > > mri_gtmpvc --i subject/dtrecon/adc.nii.gz --reg > subject/dtrecon/register.lta --psf 0 --seg subject/mri/gtmseg.mgz > --default-seg-merge --auto-mask PSF .01 --mgx 0.25 --o > subject/dtrecon/adc.pvc.mgz --no-rescale > > Thank you! > > > > On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve > <gr...@nmr.mgh.harvard.edu> wrote: > > > 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 <mailto: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 > <mailto: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 <mailto: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 <mailto: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 > <mailto: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 > <http://www.partners.org/complianceline%20>. 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > > > > > > _______________________________________________ > > 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 > gr...@nmr.mgh.harvard.edu <mailto: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 <mailto: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
