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 ayendiki@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" ayendiki@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 ayendiki@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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