I reinitialised the tracts and they all make sense now :) Hope to see you all at ISMRM.
Sean Hatton Brain and Mind Research Institute University of Sydney. On 5/04/13 7:21 AM, "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> wrote: > >It's the pathstats.byvoxel.txt file. > >On Thu, 4 Apr 2013, Sean Hatton wrote: > >> 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 FreeviewŠ <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
