Dear Anastasia, I am visually inspecting the output of Tracula, and checking the stats on pathstats.overall.
For example, in the following image (S_23_...) it can be seen that the rh.slfp is missing (there is just a very small piece of it). The rest of the tracts seem to be ok. In the stats the four xx_Avg_Center values are a NaN, and the value of the volume and Len_xx are the same, excepting Len_Center, which is zero. Although there are more statistics, I understand we should convert the whole line to NaN and not include the data of this specific subject/tract in the statistics, right? (and should I script it to make it happen always? - I mean, always that there is Len_Center=0, make everything NaN - ). [image: Inline image 5] I did freeview dpath/rh.slfp_PP_avg33_mni_bbr/path.pd.nii.gz as recommended in a the email list, and the path looks exactly like in this image.
In the next image (S_13_...) there are more problems. -- rh.slft missing (not showing in the image). Len_Center=0 again. -- fmajor almost not there, but Len_Center=1 -- lh.ccg much shorter than the rh.ccg -- very strange looking rh.cab
[image: Inline image 6] Should I consider all those tracts out of the statistics? Is there any way to mend those? (if yes, where can I find documentation?)
And last question: I understand that I could control the volume of the tracts with ICV as it is done for other volumes, but, should I control for the FA values? What exactly is FA_Avg_Weighted? (sorry, couldn't find any documentation on that while searching).
Thank you very much again and sorry for long post!
Gari
PS note that I plotted the hippocampus as well because I am analyzing it in the same study.
