There are no extreme outliers (only 3 moderate outliers). Regarding the position, is that the FA "center" measures?
Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> wrote: 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 >>> >>> >>> >>> >>> >>> >>> >> 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. >> >> >> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
