Hi Gari - What you're describing is something that may happen if the initialization of the tract fails. You can repeat with a different initialization by adding "set reinit = 1" and rerunning the -prior and -path parts. You should do this only for the subject and tract that has this issue, so set pathlist to that tract only.
If a subject has several tracts that went wrong like that, it maybe that something else is wrong, either with the aparc+aseg from the freesurfer recon, or with its registration to DWI space. So I'd check on that.
Since FA is not in units of length/surface/volume, there's no need to normalize it with another measure in such units. The "weighted averages" in the stats file are essentially the mean values in a probabilistic sense. That is, the value of the FA at each voxel is mutiplied with the probability at that voxel (from path.pd.nii.gz).
Hope this helps, a.y
On Sat, 12 Oct 2013, Garikoitz Lerma-Usabiaga wrote:
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 - ). 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
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.