Dear Anastasia, Thank you very much for your answer. In my analysis I have two groups 23 patients and 27 controls. My problem right now is that this change in the results (from the output of trac-all -path -c) gave me different P values between the groups, sometimes the results are significant and sometimes it is not! Till today I repeated this analysis many times and I collected the results after 5 consecutive runs (all the tracts for all the subjects)
Recently and In order to find a solution for this problem I used the following command line to generate the mean metrics and the tracts volume:
fslstats - dti_FA.nii.gz -k path.pd_bin.nii.gz -M -V [ I binarized "path.pd.nii.gz" (the output of trac-all -path -c for every tract) using fslmaths path.pd.nii.gz -thr 0.999 path.pd_bin.nii.gz and I used this treashold to make my mask conservative as possible]
In this case I got stable numbers. i.e when I run this command line again the results are the same. Kindly is this valid? can I use "fslstats" instead of the third step in Tracula "trac-all -path -c" to calculate the mean metrics and the tract's volume?
Also what is the difference between fslstats and trac-all -path -c (technically)
I highly appreciate your support
Mohamad ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Friday, November 21, 2014 5:10 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula_critical issue
Hi Mohamad - As it's a probabilistic method that's sampling from a distribution, there is a bit of randomness built in (which should decrease as you increase the number of samples that you collect). You'll find that the the weighted average measures are the most reliable, as they are less affected by the tails of the distribution.
a.y
On Wed, 5 Nov 2014, Alshikho, Mohamad J. wrote:
Hi Anastasia, I started recently using Tracula to do tractography for my DTI data. I did the analysis exactly as mentioned in wiki. The problem is that when I am repeating the third step (trac-all -path -c ) for the same subjects to generate the statistics; Tracula is updating all the information mentioned in the file "pathstats.overal.txt" regarding the tract's volume and the tract's metrics values. Every time the output is different. I think we have a problem in the scripts or something like this?
Attached are three "pathstats.overal.txt" files for the same subject after three consecutive runs for the "trac-all -path -c" (the same subject)
Looking forward for your support Thanks