Re: [Freesurfer] Longitudinal design

Hi Tudor,

I don't think there is a way to speed things up. Let me know if you find a case where the template is blurry or has ghosts. It should not happen, but if it does it indicates a bad registratration, you'd have to run the mri_robust_template command with different parameters manually then.

Best, Martin

On 05/27/2014 06:13 PM, Tudor Popescu wrote:

Hi Martin, Wasn't sure whether you'd seen my reply below, look forward to hear back your thoughts, thanks! Tudor

On 25 May 2014 21:40, "Tudor Popescu" <tudor3@gmail.com mailto:tudor3@gmail.com> wrote:

Thanks very much Martin and Bruce. I guess I'd misread the Wiki
(my own fault, not the text's), and am glad to hear that the
longitudinal pipeline is in fact perfectly suitable for my needs
here.

Having run the first 2 steps (cross and base), I'm a bit unclear
how the output so far has to be manually inspected. It says in the
tutorial
<http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial>
that you should load each subject's base volume + surfs in
freeview and then "move back and forth a few slices". However,
even just loading each base in this manner takes ~1 min on my PC
(CoreDuo, 4GB, Ubuntu Virtualbox in Windows 7), and then moving
with PgUp/PgDn between all coronal slices (starting from the
default slice=128, going all the way posterior and then all the
way anterior) is excruciatingly slow. All of this would have to be
repeated for all my 72 subjects - is there any way to optimise
this manual inspection?

Also, if the surfs turn out to not follow the volume correctly,
presumably the thing to do is white surface correction +
re-running recon. But what should one do if, due to an erroneous
averaging between timepoints, you see blurs/ghosts in your base
template?

Many thanks!
Tudor


On 9 May 2014 21:33, Martin Reuter <mreuter@nmr.mgh.harvard.edu
<mailto:mreuter@nmr.mgh.harvard.edu>> wrote:

    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
    <mailto: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
        <http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing>
        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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