10 Dec
2015
10 Dec
'15
4:10 a.m.
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 ?
2) Does this method supply an intensity normalisation for PET images ?
Best regards, Matthieu
15 Dec
15 Dec
4:46 a.m.
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:
Dear FS experts,
- 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 ?
- Does this method supply an intensity normalisation for PET images ?
Best regards, Matthieu
12:37 p.m.
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>:
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
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 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/
12:56 p.m.
Dear Douglas,
Please see below :
2015-12-15 18:37 GMT+01:00 Douglas N Greve 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>:
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 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 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
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.
1:01 p.m.
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>:
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>>>: > > 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 ? > YesGreat ! 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> > 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> 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 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 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/
2:57 p.m.
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 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>:
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>>>: > > 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 ? > YesGreat ! 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> > 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> 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 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 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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
3:07 p.m.
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> 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>>>: > > > > 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>>>>: > > > > 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>> > > 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>> > 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>> > 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 <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
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/
18 Dec
18 Dec
6:08 a.m.
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:
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> 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>>>: > > > > 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>>>>: > > > > 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 imageis
> 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>> > > 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> 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>> > 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 <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
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-- 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/
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12:26 p.m.
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>:
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>>> 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>>>>: > > > > > > > > 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>>>>>: > > > > > > 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>>> > > > 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>>> > > 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>>> > > 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>>> > > > > 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 > > > > > > 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>> > > 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> <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>> > 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 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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12:44 p.m.
Many thanks !
Matthieu Le 18 déc. 2015 18:27, "Douglas Greve" greve@nmr.mgh.harvard.edu a écrit :
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:
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> 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>>>: > > > > 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>>>>: > > > > 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 normalisationfor
> PET images ? > > > What do you mean by intensity normalization? For uptake analysis, > people > usually use SUV (standard uptake values where the whole imageis
> scaled > by a value related to the injection mass and subject weight) or you > choose a reference structure to scale by (often called rSUVfor
> 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>> > >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> 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>> > 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 sentto
> 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 <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>
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-- 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/
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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.
11 Jan
11 Jan
4:04 a.m.
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:
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:
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
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>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>>>>: > > > > 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 normalisationfor
> PET images ? > > > What do you mean by intensity normalization? For uptake analysis, > people > usually use SUV (standard uptake values where the whole imageis
> scaled > by a value related to the injection mass and subject weight) or you > choose a reference structure to scale by (often called rSUVfor
> 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 > 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> > 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 sentto
> 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 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> 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>
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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/
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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.
12:20 p.m.
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>:
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>>: 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>>> 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>>>>: > > > > > > > > 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>>>>>: > > > > > > 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>>> > > > 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>>> > > 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>>> > > 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>>> > > > > 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 > > > > > > 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>> > > 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> <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>> > 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 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> 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 <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 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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--
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/
12:34 p.m.
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:
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>:
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>>: 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>>> 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>>>>: > > > > > > > > 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>>>>>: > > > > > > 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>>> > > > 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>>> > > 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>>> > > 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>>> > > > > 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 > > > > > > 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>> > > 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> <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>> > 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 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> 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 <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 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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-- 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/
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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
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--
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/
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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2:33 p.m.
On 01/11/2016 02:14 PM, Matthieu Vanhoutte wrote:
Dear Douglas,
Sorry if I wasn't clear. With the PVC, voxels intensities are modified, right ?
Not necessarily. The GTM does not work this way. MG and RBV do. For an ROI analysis, the GTM is by far the preferred method.
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 ?
Again, not the right question for GTM
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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--
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/
2:39 p.m.
Le 11/01/2016 20:33, Douglas N Greve a écrit :
On 01/11/2016 02:14 PM, Matthieu Vanhoutte wrote:
Dear Douglas,
Sorry if I wasn't clear. With the PVC, voxels intensities are modified, right ?
Not necessarily. The GTM does not work this way. MG and RBV do. For an ROI analysis, the GTM is by far the preferred method.
I suppose I used MG method since I specified --mgx option (I would like to do an entire cortex analysis) ? With MG PVC, voxels intensities are the modified ?
Best regards, Matthieu
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 ?
Again, not the right question for GTM
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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3:04 p.m.
Yes with MGPVC the voxel values are rescaled by the MG formula. Note that MG (and RBV) use GTM as a preprocessing step. If you average the MG output over an ROI, then it comes close to the GTM value.
On 01/11/2016 02:39 PM, Matthieu Vanhoutte wrote:
Le 11/01/2016 20:33, Douglas N Greve a écrit :
On 01/11/2016 02:14 PM, Matthieu Vanhoutte wrote:
Dear Douglas,
Sorry if I wasn't clear. With the PVC, voxels intensities are modified, right ?
Not necessarily. The GTM does not work this way. MG and RBV do. For an ROI analysis, the GTM is by far the preferred method.
I suppose I used MG method since I specified --mgx option (I would like to do an entire cortex analysis) ? With MG PVC, voxels intensities are the modified ?
Best regards, Matthieu
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 ?
Again, not the right question for GTM
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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--
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/
15 Jan
15 Jan
4:22 a.m.
Dear Douglas,
If I understand well no PVC corrected pet images from any method (MG,RBV or GTM) have corrected white matter values ? Where do you get the pons intensity,that has been PVC'ed, used to normalize ?
Best regards, Matthieu
2016-01-11 21:04 GMT+01:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
Yes with MGPVC the voxel values are rescaled by the MG formula. Note that MG (and RBV) use GTM as a preprocessing step. If you average the MG output over an ROI, then it comes close to the GTM value.
On 01/11/2016 02:39 PM, Matthieu Vanhoutte wrote:
Le 11/01/2016 20:33, Douglas N Greve a écrit :
On 01/11/2016 02:14 PM, Matthieu Vanhoutte wrote:
Dear Douglas,
Sorry if I wasn't clear. With the PVC, voxels intensities are modified, right ?
Not necessarily. The GTM does not work this way. MG and RBV do. For an ROI analysis, the GTM is by far the preferred method.
I suppose I used MG method since I specified --mgx option (I would like to do an entire cortex analysis) ? With MG PVC, voxels intensities are the modified ?
Best regards, Matthieu
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 ?
Again, not the right question for GTM
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. Thefile 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 orafter
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 thepartial
>> 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 termsof
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:). Whenyou run
>> gtmseg, it will >> > create the new segmentation that includepons and
a few >> other things >> > >> > On 12/15/2015 12:56 PM, Matthieu Vanhouttewrote:
>> > > 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, MatthieuVanhoutte
wrote: >> > > > Dear experts, >> > > > >> > > > Could anyone answer to my questionsbelow ?
>> > > > >> > > > Thanks ! >> > > > >> > > > Best regards, >> > > > Matthieu >> > > > >> > > > 2015-12-10 10:10 GMT+01:00 MatthieuVanhoutte
>> > > > <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 usethe
partial >> volume >> > correction >> > > > provided in the v6 beta versionof
>> FreeSurfer despite >> > the fact >> > > > that recon-all have been donefor all
>> subjects with >> > the v5.3 ? >> > > > >> > > Yes >> > > >> > > >> > > Great ! but isn't it a problem forcomputing 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 anintensity
>> 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 injectionmass and
>> subject weight) >> > or you >> > > choose a reference structure to scaleby (often
>> called rSUV for >> > > relative). By default mri_gtmpvc usespons, but
>> you can >> > choose any >> > > structure you want with the --rescaleflag
>> > > >> > > > >> > > > >> > > > 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 isintended only
>> for the >> > person to >> > > whom it is >> > > addressed. If you believe this e-mailwas
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 patientinformation,
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 thePartners
> Compliance HelpLine at >http://www.partners.org/complianceline . If the e-mail wassent to
> you in error > but does not contain patient information, pleasecontact 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>
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-- 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/
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11:24 a.m.
GTM corrects for all ROIs, including WM and pons. The GTM is always run and so pons is always available for normalization. RBV is derived from the GTM so is also corrects in WM. MG does not correct in WM.
On 01/15/2016 04:22 AM, Matthieu Vanhoutte wrote:
Dear Douglas,
If I understand well no PVC corrected pet images from any method (MG,RBV or GTM) have corrected white matter values ? Where do you get the pons intensity,that has been PVC'ed, used to normalize ?
Best regards, Matthieu
2016-01-11 21:04 GMT+01:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
Yes with MGPVC the voxel values are rescaled by the MG formula. Note that MG (and RBV) use GTM as a preprocessing step. If you average the MG output over an ROI, then it comes close to the GTM value. On 01/11/2016 02:39 PM, Matthieu Vanhoutte wrote: > Le 11/01/2016 20:33, Douglas N Greve a écrit : >> On 01/11/2016 02:14 PM, Matthieu Vanhoutte wrote: >>> Dear Douglas, >>> >>> Sorry if I wasn't clear. With the PVC, voxels intensities are modified, >>> right ? >> Not necessarily. The GTM does not work this way. MG and RBV do. For an >> ROI analysis, the GTM is by far the preferred method. > I suppose I used MG method since I specified --mgx option (I would > like to do an entire cortex analysis) ? > With MG PVC, voxels intensities are the modified ? > > Best regards, > Matthieu >>> 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 ? >> Again, not the right question for GTM >>> 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> >>>>> <mailto: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>> >>>>> > <mailto: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>> >>>>> <mailto: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>>> >>>>> >> > <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>>>>> 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>>>> >>>>> >> > > <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 <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>>>>> >>>>> >> > > <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 <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>>>> >>>>> >> > > <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 <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>>>> >>>>> >> > <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 <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>>>> >>>>> >> > <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> >>>>> >> > > >>>>> >><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> >>>>> >> > > >>>>> >> >>>>> <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>>>> >>>>> >> > <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 <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>>> >>>>> >> > <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 >>>>> >> > >>>>> >> > -- >>>>> >> > 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>> >>>>> >> > 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> >>>>> >> > >>>>> <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 >>>>> >> > >>>>> >> > >>>>> >> > >>>>> >> > _______________________________________________ >>>>> >> > 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> >>>>> >> 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> >>>>> >><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>> >>>>> >> <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>> >>>>> <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>> >>>>> >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 >>>>> Fax: 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> >>>>> 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 >>> >>> > > > > _______________________________________________ > 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/
3791
Age (days ago)
3827
Last active (days ago)
freesurfer@nmr.mgh.harvard.edu
19 comments
3 participants
participants (3)
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Douglas Greve -
Douglas N Greve
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Matthieu Vanhoutte