Still using rigid-body registration on --long subject directory ? Or is affine registration in this case needed ?
Best regards, Matthieu 2016-11-14 17:12 GMT+01:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > 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:matthieuvanhoutte@ > 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:matthieuvanhoutte@ > 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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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:freesur...@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 >
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