Hi Amanda - These are probability distributions, so this has to do with how you threshold them. When you use the -tv option in freeview to open the merged file with all tracts, each of them is thresholded at 20% of its maximum. When you open one of them as a plain volume, freeview doesn't do that thresholding.
Best, a.y
On Fri, 2 Oct 2015, Worker, Amanda wrote:
Hi all,
I'm just visualising tracts that have been processed using TRACULA and I'm noticing some differences that seem slightly odd. For example, when I load the ILF for one subject, the pathway looks huge and takes up a very large portion of the brain. However, when I load the same tract along with all of the other tracts it looks like a well segmented region.
I have checked my registration with the T1 and it looks good, so I'm not sure why there is a difference. Looking at the stats for this tract volumes range from 300-600 approx. This is a patient vs control study so I would expect some differences in volume, but this seems like a big difference from the example given on the wiki which is around 160. But the average MD and FA seem reasonable and consistent at around 0.0008 and 0.4.
This is the same for many of the subjects - would you base your quality control on the visualisation of the single tracts or all of the tracts loaded together. Is there an obvious difference/ why would they load differently?
I have attached some screenshots so that you can see what I mean.
Thanks in advance.
Amanda