Hi,

I am trying to computer the changes of cortical parcellations and fiber pathways using FreeSurfer v5.3 and Tracula (2014/05/26 update) . I copied the anatomical and DWI images from the same scan session into five directories. Run recon-all and trac-all on the 5 same data sets, in order to check the reproducibility of the analysis. 

Here are what I got: the Desikan-Killiany parcellations in both GM and WM, and the subcortical structures, repeat well. No difference found in volume or size of those structures. However, the volume and averaged DTI parameters of the fiber pathways, which found in the file ~/sub/dpath/*_PP_avg33_mni_flt/pathstats.overall.txt, varies for the 5 sets.   tracula.conf files were copied from ~/freesurfer/bin/dmrirc.example.

The changes are calculated in percentage by (S1-S0)/((S1+S0)/2)*100%. For example, the changes of averaged FA  between the 5 data sets are :
                                                                                                             S1-S0, S2-S0, S3-S0, S4-S0
Corpus Callosum - Forceps Major                                          ,   -1.1   ,    6.0   ,    0.5   ,    1.3   ,
Corpus Callosum - Forceps Minor                                          ,    0.1   ,    0.0   ,   -1.6   ,    0.0   ,
Right Anterior Thalamic Radiations                                        ,    0.1   ,   -1.0   ,    0.5   ,    0.9   ,
Right Cingulum - Angular Bundle                                            ,   -4.8   ,   -2.0   ,   -1.5   ,    3.8   ,
Right Cingulum - Cingulate Gyrus Endings                            ,    0.5   ,   -0.9   ,    0.4   ,   -2.3   ,
Right Corticospinal Tract                                                            ,    1.9   ,    0.6   ,   -2.2   ,    1.4   ,
Right Inferior Longitudinal Fasciculus                                     ,   -2.2   ,   -0.8   ,   -1.3   ,    3.0   ,
Right Superior Longitudinal Fasciculus - Parietal Endings ,    0.8   ,   -0.4   ,   -1.2   ,    0.2   ,
Right Superior Longitudinal Fasciculus - Temporal Endings ,   -4.9   ,   -0.6   ,   -2.6   ,   -1.3   ,
Right Uncinate Fasciculus                                                              ,    0.5   ,    1.6   ,   -0.9   ,    3.5   ,


Even larger changes for the volume of the pathways:
                                                                                                              S1-S0, S2-S0, S3-S0, S4-S0
Corpus Callosum - Forceps Major                                            ,    2.2   ,  -33.7   ,  -12.3   ,    1.1   ,
Corpus Callosum - Forceps Minor                                            ,   11.9   ,    4.8   ,    0.6   ,    7.2   ,
Right Anterior Thalamic Radiations                                          ,   -8.9   ,    2.2   ,  -12.5   ,    7.5   ,
Right Cingulum - Angular Bundle                                               ,  -38.1   ,   41.6   ,   34.8   ,    8.6   ,
Right Cingulum - Cingulate Gyrus Endings                              ,   24.4   ,   33.1   ,   21.3   ,   17.5   ,
Right Corticospinal Tract                                                              ,    9.8   ,   -3.0   ,    2.2   ,   19.5   ,
Right Inferior Longitudinal Fasciculus                                      ,    7.2   ,   24.1   ,   -7.3   ,   23.8   ,
Right Superior Longitudinal Fasciculus - Parietal Endings  ,   17.2   ,   10.2   ,   25.1   ,    9.9   ,
Right Superior Longitudinal Fasciculus - Temporal Endings ,   15.4   ,    3.4   ,   -3.1   ,  -11.5   ,
Right Uncinate Fasciculus                                                                ,   13.3   ,   -1.2   ,   16.4   ,   -3.4   ,

Any expert has the experience on these? Thank you for your help.

XJ Kang