Hi Sarah,
you deal with the time during post-processing (statistical analysis).
Yes, you have differently many rows for each subject. Years could be time from baseline, or time from start of study (e.g. start of drug treatment). It may be the same, but if some subjects are missing the baseline scan in a drug study it may be better to use the start of the drug instead of the first scan.
Mixed effects model is the way to go.
Best, Martin
On 03/06/2013 05:17 PM, Sarah Whittle wrote:
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 [mreuter@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
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-- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
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