Hello Martin,

Thank you for your swift reply.

I failed to make myself clear, and will try describing my study again. First, an important point: the study is not longitudinal per se, but I am interested in applying the methods of longitudinal analysis. I only have one time point, all the scans have been collected within the same session.

I am studying a large group of subjects whom each underwent a scan session with 4 scans. Each of these scans were graded for quality on a scale from 1-4.
An example of what I then did was to process each subject twice, once with the scan of quality ”1”, and a second time averaging the scans of quality ”1” and ”2”, thus resulting in two groups between which each subject is compared to itself.

Now I am attempting to set up a longitudinal analysis with this data. I have processed through the longitudinal stream, and I guess my question starts at the point of post-processing: How, if feasible, can I transfer the idea of “across group comparison between time point and time point 2” to “across group comparison between 1 scan and 2 scans” in setting up the QDEC table and continuing from there?

I hope this make sense, your help is greatly appreciated.

Best regards,

Joy-Loi





On 2013-03-18 19:13, Martin Reuter wrote:

Hi Joy-Loi,
so you have 2 time points? the first with a single scan, the second
with two within-session scans that you want to average? I don't
understand exactly what you are trying to do.  To test differences in
reliability you'd have to scan a bunch of subjects twice in a session
and then twice in another session.
Then you can look at reliability when using only one scan (e.g. the
first) or when averaging both scans in both time points. 'varying
quality' with respect to motion also scares me a little. There can be
individual outliers that severely affect your mean response (unless
you have lots of subjects).
Anyway for these things you would process your results through the
longitudinal stream (this allows you also to be unbiased with respect
to the time point). There are several design questions to consider
(e.g. does it make sense to include all virtual time points into the
same base, or run everything twice: one base for the averaged images ,
another for the single images and then compare etc. ) Either way this
is not a standard analysis and you'd be pretty much on your own with
how to set it up.
Best, Martin
On 03/18/2013 09:02 AM, Joy-Loi Chepkoech wrote:

Hello FreeSurfer experts,
I am currently trying to systematically investigate the differences in
cortical and subcortical estimates that occur when performing recon-all
on one scan, or when averaging across scans of varying quality with
regard to movement.
I have a list of subjects that each have been processed (recon-all)
twice (once with one scan and once with two scans), and would like to
run some FreeSurfer statistical analysis on them.
Is it feasible to set up a longitudinal analysis similar to the one
described here:
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial)?
If it is, could someone assist me in setting this analysis up?
(I have tried following the tutorial, where I on each subject set "0
years" for one scan, and "1 year" for two scans in the QDEC table, but
the results from the QDEC analysis don't seem to agree with previous
SPSS results that I have).
Thank you,
Joy-Loi
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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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