11 Jan
2016
11 Jan
'16
2:14 p.m.
Dear Douglas,
Sorry if I wasn't clear. With the PVC, voxels intensities are modified, right ? So, in the case of anatomical intensity normalization based on gray matter of cerebellum, is the mean activity of gray cerebellum taken from the original PET image or from the PVC'ed PET image ?
Best regards, Matthieu
Le 11/01/2016 18:52, Douglas N Greve a écrit :
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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" >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 >> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> >> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 >> > > > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> >> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> >> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> >> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> >> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> >> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> >> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> >> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>> >> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> >> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> >> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> >> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> >> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> >> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> >> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> >> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@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 >> > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> >> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 >> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 >> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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
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