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Dear imaging experts..

I apologized that my questions are not directly related to FSL processing.
Hope someone can help me as for the followings;
1) Using fslvbm, I compared GM volume between two groups of subjects (a neurodegenerative disease patients with normal visual processing vs. same disease patients with abnormal visual processing on a same taske). The other confounders (eg, demographics, education years, disease duration and severity, MMSE, depression scale, language function, and so forth) are not different between the groups. I have obtained somewhat satisfactory results in both statistical and interpretation grounds (ie, decreased GM volume in the expected cortex). 
However, this is the preliminary study and hence we did not yet include control subjects (ie, no brain disorder, normal cognitive function). I know that VBM study basically started from between-group comparison of patients and controls. In this regard, is this result not appropriate for submission to the jounal? Must I further include control subjects and reanalyze the MR data?

2) Here is another question. I'm pretty interested in cortical thickness analysis. As far as I know there is no tool available in FSL, right? I know that 'Freesurfer' is a wonderful software but seems hard for me to use. Moreover, Brainvoyager also provide cortical thickness analysis, but it is only commercially available. 
Is there a more 'easy-to-learn' free toolkit for cortical thickness analysis? If yes, please let me know.


Many thanks in advance for your valuable advices.

Kim