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 <tud...@gmail.com
<mailto:tud...@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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Martin Reuter, Ph.D.
Instructor in Neurology
Harvard Medical School
Assistant in Neuroscience
Dept. of Radiology, Massachusetts General Hospital
Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
Computer Science and Artificial Intelligence Lab,
Dept. of Electrical Engineering and Computer Science,
Massachusetts Institute of Technology
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
