Thanks Martin and Nick, We have a number of subjects with single time points too, so I think 5.2 is the best way to go.
Is there a way to specify which subjects have data at what time points. For example, if one subject has data at Time 1 and Time 3, and another has data at Time 2 and Time 3, can this info be fed into freesurfer somehow? Or, do you just deal with this during post processing by specifying the years between scans (which would be different for these two cases)? Also, when creating the longitudinal .dat file, I assume you would have a different number of rows for each subject depending on how many time points they have, and the value you would enter for 'years' would just be years since baseline? Finally, can you use QDEC with three time points? Or would linear mixed effects models be the way to go? Thanks, Sarah ________________________________________ From: Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: Thursday, 7 March 2013 5:41 AM To: Nick Schmansky Cc: Sarah Whittle; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint Hi Sara, yes, should work, just make sure that all cross are 5.1 (and not mixed) to remain consistent. By the way 5.1 can process differently many time points for each subject. Just not subjects with a single time point only. To include those you'd need 5.2 Best, Martin On 03/06/2013 01:32 PM, Nick Schmansky wrote: > Sarah, > > I'm cc'ing martin reuter on this, but yes, you should be able to use > your cross-sectionally processed scans from v5.1 in a longitudinal > analysis using v5.2. > > Nick > > > On Wed, 2013-03-06 at 05:46 +0000, Sarah Whittle wrote: >> Hi, >> >> RE the below post, we have longitudinal data from three time points, >> but a number of participants have scans for only one or two time >> points. We've done all of the cross-sectional analysis (including a >> lot of manual editing) and are ready to run everything through the >> longitudinal stream. Our plan was to run sets of analyses for all of >> the possible combinations of longitudinal scans. >> >> e.g., Time 1, Time 2, Time 3; >> Time 1, Time 2; >> Time 1, Time 3; >> Time 2, Time 3 >> >> Obviously the new feature in version 5.2 (i.e., being able to run all >> images together, regardless of whether some time points are missing >> for some people) would be MUCH better. Is this possible to do using >> our 5.1 cross-sectionally processed images? Given the time we've put >> into manual editing, we really wouldn't want to have to run everything >> again through 5.2. >> >> Thanks, >> >> Sarah >> >> .... >> Hi Henk-Jan, >> >> to avoid bias between subjects with single time points and others, we >> run them through the same steps. This way it is possible to include them >> into the statistical analysis. (For this an artificial base is created >> with the head in an upright and straight position). >> >> This feature will be available in 5.2. Nothing with respect to >> processing commands changes, you will simply pass only a single time >> point to the -base and then run it with -long. >> Nice and transparent :-). >> >> Anyway, you probably should wait till 5.2. There is several programs >> that changed for this to work. Also the current recon-all contains many >> changes not related to this. If you absolutely cannot wait, let me know >> and I'll take a look at how difficult it is to go back and adjust 5.1. >> >> Best, Martin >> >> >> >> On Tue, 2012-12-04 at 17:06 +0000, Westeneng, H.J. wrote: >>> Hi Freesurfer experts, >>> >>> >>> >>> This week a read the article of Bernal-Rusiel et al. titled >>> “Statistical analysis of longitudinal neuroimage data with Linear >>> Mixed Effects models”. In this article you described the submission of >>> single time-point scans to the longitudinal pipeline of Freesurfer. >>> I’m very interested in how to do this. Your help will be appreciated. >>> >>> >>> >>> Thanks in advance, >>> >>> >>> >>> Henk-Jan >>> >>> >>> >>> ______________________________________________________________________ >>> >>> De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is >>> uitsluitend bestemd voor de geadresseerde. Indien u dit bericht >>> onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de >>> afzender direct te informeren door het bericht te retourneren. Het >>> Universitair Medisch Centrum Utrecht is een publiekrechtelijke >>> rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en >>> Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van >>> Koophandel voor Midden-Nederland onder nr. 30244197. >>> >>> Denk s.v.p aan het milieu voor u deze e-mail afdrukt. >>> >>> >>> ______________________________________________________________________ >>> >>> This message may contain confidential information and is intended >>> exclusively for the addressee. If you receive this message >>> unintentionally, please do not use the contents but notify the sender >>> immediately by return e-mail. University Medical Center Utrecht is a >>> legal person by public law and is registered at the Chamber of >>> Commerce for Midden-Nederland under no. 30244197. >>> >>> Please consider the environment before printing this e-mail. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer at 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 > > -- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu The information in this e-mail is intended only for the person to whom it is addressed. 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