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" <tud...@gmail.com
<mailto:tud...@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 <mreu...@nmr.mgh.harvard.edu
<mailto:mreu...@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 <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
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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
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