SUVR you can. BP is a little trickier because BP estimation is a nonlinear operation that can be biased by noise. Probably it comes out similarly.
On 08/16/2017 02:50 PM, Shane Schofield wrote: > Hi Dr Greve, > > On a similar note, can I use the Petsurfer on PET data that have > already been averaged into a single frame 3D volume instead of 4D? > Example, SUVR and BPND data. > > Thanks for your help again. > > > On Tuesday, August 15, 2017, 9:09:33 AM GMT+1, Shane Schofield > <shane.schofi...@yahoo.com> wrote: > > > Hello Dr Greve, > > I have ran the command and got the data from the gtm.stats.dat. > However, all the values are 0.001 - 0.003. Can I scale it up or show > the data with more precision? > > Thank you. > > > On Monday, August 14, 2017, 9:31:38 PM GMT+1, Douglas N Greve > <gr...@nmr.mgh.harvard.edu> wrote: > > > 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 <mailto: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> > <mailto: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> > > <mailto: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> <mailto: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> > <mailto: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> > > <mailto: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> > > <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> > <mailto: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> > <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 > > 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> > <mailto: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
