The increase in FA in patients is strange indeed. Are there any outliers
in the tract averages? (Sorry if you've already mentioned this.)
There are definitely situations in which TBSS and tracula would give you
different results, since tracula gives you average FA in a large bundle,
whereas TBSS gives voxel-based differences, where the voxels are on the
skeleton of the white matter. So you could imagine a situation where part
of a tract shows a decrease and other parts don't. Have you looked at the
FA as a function of position along the tract from tracula (the other stats
file that it gives you)?
On Thu, 4 Apr 2013, Sean Hatton wrote:
Yes, TBSS has reductions in FA in the patients' ATR cf controls (TFCE corrected,
p<. 05), but extracting the path stats in Tracula have the patients' ATR FA
increased cf controls (independent t test, p<. 05, uncorrected as per Yendiki et
al. 2011).
Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> wrote:
Hm, it doesn't sound like a failure in the tract reconstruction then. What
areas does TBSS give you differences in? Is it in the area of the same
tracts?
On Thu, 4 Apr 2013, Sean Hatton wrote:
Hi Anastasia,
An independent T-test on the aseg.stats "WM-Hypointensties" (SegId 77) showed
that the
mean WM hypointensities volume of the patient group (1378.8mm3, SD 650mm3) did
not
significantly differ from the controls (1120.8mm3, SD 372mm3; p=.111). A
Pearson and
Spearman correlation analysis found no correlation of WMH volume with tract
volumes
but did find a correlation with FA in three of the nine tracts of interest
(Forceps
minor, left ATR, left ILF). I reviewed the T2-FLAIRs for the subjects with the
highest
volumes of WM lesions and they were all dirty-appearing white matter around the
ventricles rather than punctate WMH within the regions of these tracts.
The tracts look reasonable in Freeview… <scratching head>
Sean
On 4/04/13 7:17 AM, "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> wrote:
Hi Sean - Can you check their freesurfer aseg's and see if any of the
white matter was classified as a hypointensity there?
a.y
On Wed, 3 Apr 2013, Sean Hatton wrote:
This is Tracula 5.2 with FLIRT and the vectors are correctly aligned
(V1 over FA).
From the literature and what is seen in my TBSS is reduced FA in the minor
forceps and
ATR.
These are young (23yo) psychiatric so age related atrophy is not expected.
However,
they are known to have WM hypointensities even at a young age, I can
review their T2s.
A few are on mood stabilizers, but if this affected FA I would also see it
in TBSS.
Thoughts?
Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> wrote:
Oh, another question: do your patients have white-mater
hypo/hyper-intensities, in other words any voxels in the white matter that
are classified as something other than white matter in the freesurfer
aseg?
On Wed, 3 Apr 2013, Sean Hatton wrote:
Hi Freesurfer gurus,
I have been using Tracula to investigate white matter abnormalities in a
patient
cohort (n=20) compared to matched controls (n=40). In line with the
literature, we
expected to see reductions in FA in the patients' tracts but instead
they have
significantly higher FA means. To double-check, we ran TBSS over the
same cohorts
and
got the results as per the literature (I.e. reduced FA in the patient
group). The
FA,
RD, AD, MD and volume outputs are normally distributed and there are no
extreme
outliners. So wondering:
1. The patient group had significantly reduced tract volumes. If this
volume
calculation is incorrect I expect it could influence the calculation
of the mean
FA, RD, AD etc. Is there a way of checking the volume and subsequent
calculations?
2. Yendiki et al 2011 had no corrections – do I need corrections?
3. Should I be thresholding tract stats?
Thank you in advance,
Sean Hatton
Brain and Mind Research Institute
University of Sydney
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