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It’s hard to know from that context what they are referring to.  Perhaps if you posted a larger quote of the comment someone could figure out what the reviewer meant.

Peace,

Matt.

From: Abbie Williams <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Monday, July 7, 2014 at 2:40 AM
To: <[log in to unmask]>
Subject: [FSL] weakness

Dear all,

I am using FSL for a DTI analysis. In a paper revision I have been told that TBSS has weaknesses on revealing tract-specific features. 
I am not sure what does it mean. Could anyone help me?

Thanks in advance. 
Regards,
Abbie