Dear Douglas, Just one more question : by default mri_gtmpvc uses pons for computing rSUV, but is this intensity normalization done before or after partial volume correction ? What file is used in input for intensity normalization ?
Thanks in advance ! Best regards, Matthieu 2015-12-18 18:26 GMT+01:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>: > You'll see several files that begin with mgx: > mgx.ctxgm.nii.gz - pvc'ed cortex gm only > mgx.subctxgm.nii.gz - pvc'ed subcortical gm only > mgx.gm.nii.gz - pvc'ed all gm > > > On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote: > > Hello Douglas, > > I have run mri_gtmpvc with static PET images using the following command : > mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg gtmseg.mgz > --reg register.dof6.lta --default-seg-merge --mgx 0.01 --o gtmpvc.output > > In the output directory "gtmpvc.output" where is the partial volume > corrected PET image ? > > Thanks ! > > Best regards, > Matthieu > > 2015-12-15 21:07 GMT+01:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > >> Not necessarily. It needs a good segmentation, so, to the extent that v6 >> has a better segmentation then v6 is better. >> >> On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote: >> > >> > Thanks Douglas for the answer ! >> > >> > But isn't PVC design for better working in terms of results with >> > v6_beta than v5.3 ? >> > >> > Best regards, >> > >> > Matthieu >> > >> > Le 15 déc. 2015 19:02, "Douglas N Greve" < <gr...@nmr.mgh.harvard.edu> >> gr...@nmr.mgh.harvard.edu >> > <mailto:gr...@nmr.mgh.harvard.edu>> a écrit : >> > >> > It is not subsegmented in 6.0 either:). When you run gtmseg, it will >> > create the new segmentation that include pons and a few other things >> > >> > On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote: >> > > Dear Douglas, >> > > >> > > Please see below : >> > > >> > > 2015-12-15 18:37 GMT+01:00 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>gr...@nmr.mgh.harvard.edu>>>: >> > > >> > > >> > > >> > > On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote: >> > > > Dear experts, >> > > > >> > > > Could anyone answer to my questions below ? >> > > > >> > > > Thanks ! >> > > > >> > > > Best regards, >> > > > Matthieu >> > > > >> > > > 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte >> > > > <matthieuvanhou...@gmail.com >> > <mailto:matthieuvanhou...@gmail.com> >> > > <mailto:matthieuvanhou...@gmail.com >> > <mailto:matthieuvanhou...@gmail.com>> >> > > <mailto:matthieuvanhou...@gmail.com >> > <mailto:matthieuvanhou...@gmail.com> >> > > <mailto:matthieuvanhou...@gmail.com >> > <mailto:matthieuvanhou...@gmail.com>>>>: >> > > > >> > > > Dear FS experts, >> > > > >> > > > 1) First Is it possible to use the partial volume >> > correction >> > > > provided in the v6 beta version of FreeSurfer despite >> > the fact >> > > > that recon-all have been done for all subjects with >> > the v5.3 ? >> > > > >> > > Yes >> > > >> > > >> > > Great ! but isn't it a problem for computing rSUV with pons as >> > > reference structure since brainstem isn't sub-segmented in the >> > version >> > > 5.3 of recon-all ? >> > > >> > > > >> > > > >> > > > 2) Does this method supply an intensity normalisation >> for >> > > PET images ? >> > > > >> > > What do you mean by intensity normalization? For uptake >> > analysis, >> > > people >> > > usually use SUV (standard uptake values where the whole image >> is >> > > scaled >> > > by a value related to the injection mass and subject weight) >> > or you >> > > choose a reference structure to scale by (often called rSUV >> for >> > > relative). By default mri_gtmpvc uses pons, but you can >> > choose any >> > > structure you want with the --rescale flag >> > > >> > > > >> > > > >> > > > Best regards, >> > > > Matthieu >> > > > >> > > > >> > > > >> > > > >> > > > _______________________________________________ >> > > > 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> >> Freesurfer@nmr.mgh.harvard.edu>> >> > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > -- >> > > >> > > >> > > Best regards, >> > > Matthieu >> > > >> > > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >> > > 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> >> > > 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> >> 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 >> > <mailto: <Freesurfer@nmr.mgh.harvard.edu> >> 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 <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: https://gate.nmr.mgh.harvard.edu/filedrop2 >> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > <http://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 >> > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 > > > 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. > >
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