I would just register the pet to the closest (in time) anatomical
On 11/14/2016 07:20 AM, Matthieu Vanhoutte wrote: > Dear Freesurfer's experts, > > I come back to you concerning questions of registrations. > > Since during the longitudinal process each --long subject directory > has been registered onto the common --base template, shouldn't I: > > 1) Register PET data onto the subject cross-sectional directory > (native data) with rigid-body transformation > 2) Then take into account the registration between --cross and --long > directory subject and apply the registration to the PET first > registered onto native space ? In this case, how and where is this > transformation has been saved ? > > Best regards, > Matthieu > > 2016-09-30 23:05 GMT+02:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>: > > Yes > > > On 09/30/2016 05:05 PM, Matthieu Vanhoutte wrote: > > > > Hi Douglas, > > > > Does the surface of the closest MRI time point mean the surface > of the > > -long subject time point directory rather than cross-sectional > subject > > time point directory ? > > > > Best regards, > > Matthieu > > > > > > Le 30 sept. 2016 9:14 PM, "Douglas N Greve" > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> a écrit : > > > > There is no such long process for PET. The idea is that you > > process the > > MRI in a longitudinal way, then sample the PET data onto the > > surface of > > the closest MRI time point. Then proceed in a way similar to the > > thickness analysis > > > > > > On 09/29/2016 11:08 AM, Matthieu Vanhoutte wrote: > > > Dear Freesurfer's experts, > > > > > > Could you answer me about my last question with no > response in the > > > mail below ? > > > > > > When using cortical thickness in longitudinal analysis > with LME, we > > > used lh.thickness or rh.thickness from -long subject > directories. > > > These data followed particular processing steps including > > > registrations in order to use them with more precision in > > longitudinal > > > studies, didn't they ? > > > > > > My problem is that I would like to perform longitudinal > study on PET > > > data images with LME. So I wonder if I just have to > resample onto > > > -long cortical subject surface ? Do I need to follow the > same steps > > > than cortical thickness from cross-sectional to -long subject > > > directories ? If this is the case, which commands should I > use to > > > mimic cortical thickness longitudinal data ? > > > > > > Many thanks in advance for helping ! > > > > > > Best regards, > > > Matthieu > > > > > > 2016-09-18 23:02 GMT+02:00 Matthieu Vanhoutte > > > <matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com> > > <mailto:matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com>> > > <mailto:matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com> > > <mailto:matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com>>>>: > > > > > > Hi Martin, > > > > > > Thanks for your answer. However, it seems to me that > cortical > > > thickness follow a particular process with the > recon-all -long > > > process, isn’t it ? Is there any resample onto average > time > > > subject then other operation following ? > > > > > > Best regards, > > > Matthieu > > > > > > > Le 18 sept. 2016 à 16:26, Martin Reuter > > > <mreu...@nmr.mgh.harvard.edu > <mailto:mreu...@nmr.mgh.harvard.edu> > > <mailto:mreu...@nmr.mgh.harvard.edu > <mailto:mreu...@nmr.mgh.harvard.edu>> > > <mailto:mreu...@nmr.mgh.harvard.edu > <mailto:mreu...@nmr.mgh.harvard.edu> > > <mailto:mreu...@nmr.mgh.harvard.edu > <mailto:mreu...@nmr.mgh.harvard.edu>>>> > > > a écrit : > > > > > > > > Hi Matthieu, > > > > > > > > I never used PET data, but once you manage to > resample you pet > > > data onto the surface, you will have a file similar to the > > > thickness file for each subjects. Instead of thickness > it holds > > > you PET information. From that point on everything > should be > > > identical to the thickness analysis. > > > > > > > > So this is really more a question how to get your > PET data > > > sampled onto the surface. If no one else replies, > write that > > into > > > the subject line and repost. > > > > > > > > Best, Martin > > > > > > > > > > > >> On Sep 17, 2016, at 7:37 AM, Matthieu Vanhoutte > > > <matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com> > > <mailto:matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com>> > > <mailto:matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com> > > <mailto:matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com>>>> > > > wrote: > > > >> > > > >> Dear Freesurfer’s experts, > > > >> > > > >> I would like to use the longitudinal mixed-effects > model for > > > surface PET analysis. Although I could find all the > process to > > > follow the longitudinal analysis of cortical thickness, I > > couldn’t > > > resolve the steps/commands to apply successively to > coregistered > > > PET data on T1 MRI. > > > >> > > > >> Could you precise me the process and commands to > use for PET > > > longitudinal analysis ? > > > >> > > > >> Many thanks in advance ! > > > >> > > > >> 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 > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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. 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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 > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <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 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 > <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/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <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 > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <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/ > <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 > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
