11 Jan
2016
11 Jan
'16
12:52 p.m.
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
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
greve@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/