Hi Matthieu, 1. yes, LME needs to be done first so that values can be sampled from the fitted model for the SA.
2. yes, I was talking about gradient non-linearities etc that could be in the image from the acquisition. We currently don’t use non-linear registration across time points (only rigid). Best, Martin > On Nov 22, 2016, at 9:31 PM, Matthieu Vanhoutte <matthieuvanhou...@gmail.com> > wrote: > > Hi Martin, > > Please see inline below: > >> Le 22 nov. 2016 à 17:04, Martin Reuter <mreu...@nmr.mgh.harvard.edu >> <mailto:mreu...@nmr.mgh.harvard.edu>> a écrit : >> >> Hi Matthieu, >> (also inline) >> >>> On Nov 21, 2016, at 10:28 PM, Matthieu Vanhoutte >>> <matthieuvanhou...@gmail.com <mailto:matthieuvanhou...@gmail.com>> wrote: >>> >>> Hi Martin, >>> >>> Thanks for replying. Please see inline below: >>> >>>> Le 21 nov. 2016 à 20:26, Martin Reuter <mreu...@nmr.mgh.harvard.edu >>>> <mailto:mreu...@nmr.mgh.harvard.edu>> a écrit : >>>> >>>> Hi Matthieu, >>>> >>>> a few quick answers. Maybe Jorge knows more. >>>> Generally number of subjects / time points etc. cannot be specified >>>> generally. All depends on how noisy your data is and how large the effect >>>> is that you expect to detect. You can do a power analysis in order to >>>> figure out how many subject / time points would be needed. There are some >>>> tools for that in the LME toolbox: >>>> https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels#Poweranalysis >>>> >>>> <https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels#Poweranalysis> >>>> >>>> >>>> 1. see above >>>> 2. yes, also time points can miss from the middle. If you have mainly >>>> missing time points at the end, this will bias your analysis to some >>>> extend, as the remaining ones may be extremely healthy, as probably the >>>> more diseased ones drop out. You may want to do a time-to-event (or >>>> survival-analysis) which considers early drop-out. >>> >>> Is there any way to do with Freesurfer this kind of analysis ? >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/SurvivalAnalysis >> <https://surfer.nmr.mgh.harvard.edu/fswiki/SurvivalAnalysis> >> Yes, there is also a paper where we do this. It is a combination of LME and >> Survival Analysis (as for the SA you need to have measurements of all >> subjects at all time points, so you estimate that from the LME model). > > Thank you for the link, I will take a look at. So if understand, this > analysis has to be done after LME statistical analysis ? Thereafter since SA > need all time points, LME model will allow me to estimate missing time points > ? > >> >>> >>>> 3. see above (power analysis) >>>> 4. GIGO means garbage in, garbage out, so the less you QC, the more likely >>>> will your results be junk. The more you QC the less likely will it be >>>> junk, but could still be. The FS wiki has lots of tutorial information on >>>> checking freesurfer recons. For longitudinal, you should additionally >>>> check the surfaces in the base, the brain mask in the base, and the >>>> alignment of the time points (although there is some wiggle space for the >>>> alignment, as most things are allowed to evolve further for each time >>>> point). >>> >>> For the alignment of the time points, should I better comparing brainmask >>> or norm.mgz ? >> >> It does not really matter, I would use norm.mgz. I would load images on top >> of each other and then use the opacity slider in Freeview to blend between >> them (that way the eye can pick up small motions). I would not worry too >> much about local deformations which could be caused by non-linearity >> (gradient). But if you see global misalignment (rotation, translation) it is >> a cause for concern) . > > Ok thank you. The non-linearity you are talking about are well provoked by > MRI system and not non-linear registration between time points and template > base, aren’t they ? > > Best regards, > Matthieu > >> >>> >>> In order to avoid bias by adding further time points in the model by the >>> -add recon all command, is this better for each subject to take into >>> account all the time points existing for it or only the ones that I will >>> include in the model (three time points / subject ; if existing 6 time >>> points for any subject ?) >>> >> >> Usually it is recommended to run all time points in the model (so a base >> with 6 time points) and not use the - - add flag. Also, Linear Mixed Effects >> models deal well with missing time points. It is perfectly OK to have >> differently many time points per subject for that. You should still check if >> there is a bias (e.g. one group always has 3 time points the other 6) that >> would not be good. Maybe also consult with a local biostatistician if you >> are not comfortable with the stats. The LME tools are matlab, and so are the >> survival-analysis scripts. >> >> Best, Martin >> >> >> >>> Best regards, >>> Matthieu >>> >>>> >>>> Best, Martin >>>> >>>>> On Nov 21, 2016, at 7:07 PM, Matthieu Vanhoutte >>>>> <matthieuvanhou...@gmail.com <mailto:matthieuvanhou...@gmail.com>> wrote: >>>>> >>>>> Dear Freesurfer’s experts, >>>>> >>>>> I would have some questions regarding the LME model to be used in >>>>> longitudinal stream: >>>>> >>>>> 1) Which are the ratio limits or % of missing timepoints accepted ? >>>>> (according time, I have less and less subjects time points) >>>>> >>>>> 2) Is it possible to include patients that would miss the first timepoint >>>>> but got the others ? >>>>> >>>>> 3) Considering a group in longitudinal study, which is the number of >>>>> subjects minimal of this group accepted for LME modeling ? >>>>> >>>>> 4) Finally, concerning quality control and among a big number of total >>>>> time points, which essential controls are necessary ? (Control of >>>>> norm.mgz of the base, alignment of longitudinal timepoints on base,… ?) >>>>> >>>>> 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 >>>>> <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> >>>> >>>> >>>> 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 >>>> <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 >>> <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> >> >> >> 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 >> <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 > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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