Hi Tudor,

the longitudinal pipeline in FS is actually one of the best on the planet as far as I know :-). If there is any contradictory information on the wiki, can you point me to that so I can see what causes the misconception. Really: compared to independent processing, it significantly increases sensitivity. Also we have designed it to be unbiased with respect to a single time point or directionality. It is quite mature by now.

You should definitely use the longitudinal pipeline for the analysis of your data. Now to your questions

1. QDEC: I am not too familiar with qdec. You can definitely try the 2-stage approach described on the wiki. There you first compute a measure of change (e.g. hippocampal volume change during your week) and then compare that measure across groups similar to a cross sectional volume/thickness analysis. You can also use our tools to run a linear mixed effects model if you want to do that (it is more involved and requires you to use matlab tools). In your case, you probably have 2 time points for all subjects and the time distance is probably the same for all subjects, so the 2-stage approach should be fine.

2. The image processing is done via the longitudinal pipeline (three steps: cross, base, long), to prepare the data look at the description of the 2-stage model
http://freesurfer.net/fswiki/LongitudinalTwoStageModel
and also the longitudinal tutorial
http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial

3. At the recon all level in FS you get (after the 3 steps) measurement for all time points. So you would compare those results across time in the stats.

Hope that helps, Martin

On 05/08/2014 08:14 AM, Tudor Popescu wrote:
Sorry for the repeat, wasn't sure whether this was received the first time.
Tudor


On 6 May 2014 19:55, Tudor Popescu <tudor3@gmail.com> wrote:
Dear FS list,

I have structural data from a learning study (pre&post-training scans, with 3 groups). Although the training was only one week, I'm guessing from an analysis point of view, this still qualifies as longitudinal. I want to check for
  • the main within-subjects effect of time point (pre&post)
  • the main between-subjects effect of group (treatment A, treatment B, control),
  • the time x group interaction
I intend to look at thickness, surface area, volume, and lGI.

I read on the wiki that FS is currently not optimal for longitudinal analyses. I intend my FreeSurfer analysis to supplement a VBM analysis done in FSL. In case it is in fact a good idea to do this, my questions (not covered in the 'longitudinal' wiki page) are:

1) Can QDEC be used for such an analysis, and if so, what would be different as compared to a cross-sectional (no temporal/within factor) study?

2) Also, is the pre-processing stage any different?

3) In FSL, for longitudinal designs you do stats on images obtained as the difference between consecutive time points. Does this have to be done in FreeSurfer as well, and if so, is it done at the recon-all level or only at the stats (QDEC) level?

Thanks!

Tudor





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Martin Reuter, Ph.D.

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