I'm not sure exactly what you mean. I guess you could set all voxels in a given ROI to be the value of that ROI? This is not really a voxel-wise correction and probably would not do what you want. You can use the mgx data (corrected with muller-gartner method). There is also a --rbv (region-based voxel-wise, Thomas 2012) option.
On 01/11/2016 12:34 PM, Matthieu Vanhoutte wrote: > Dear Douglas, > > If the pons intensity used to normalize has been PVC'ed, couldn't we > have an output of mri_gtmpvc with the whole brain PVC'ed ? > > Because the only files on output of mri_gtmpvc are : > 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 > > Best regards, > Matthieu > > 2016-01-11 18:20 GMT+01:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>: > > > The pons intensity used to normalize has been PVC'ed. The file used is > the input file. > > > On 01/11/2016 04:04 AM, Matthieu Vanhoutte wrote: > > 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 <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto: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 > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto: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 > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > >> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > >> <mailto: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>> > >> <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > >> <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > >> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > >> <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > >> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > >> <mailto:gr...@nmr.mgh.harvard.edu > <mailto: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>>> > >> > > <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 > <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> > >> <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 > <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>> > >> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> > <mailto: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 > >> > > > >> > > -- > >> > > > >> > > > >> > > 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>> > >> <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > >> <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > >> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > >> <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > >> <mailto: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>> > <tel:617-724-2358 <tel:617-724-2358> > >> <tel:617-724-2358 <tel:617-724-2358>>> > >> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> <tel: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>> > >> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>>> <tel: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> > >> > > <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> > >> > > >> > <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>> > >> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> > <mailto: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 . 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>> > >> > <mailto: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>> > >> <mailto: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> > >> > > <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> > >> > > >> > <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>> > >> <mailto: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 <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> > >> <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>> > >> 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 > > > > > > _______________________________________________ > > 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 . 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 > > -- > 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 > <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
