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Hi, Do you see any error messages in the log files? It sounds like you are experiencing some problems, which might even be unrelated to FSL if the same data works sometimes and not others. In that case it might be related to file system issues or something else. Anyway, if you are still having trouble, let us know about the log files and also tell us if you have any subject where you get a consistent problem. All the best, Mark On 7 Feb 2014, at 21:53, Renxin Chu <[log in to unmask]> wrote: > Hello Experts, > I am using run_first_all tools and try to get deep gray matter > /sub-cortical structures. The strange thing is that I can get all of > sub-cortical structures such as R_Puta, L_Puta, R_Thal, L_Thal for few > subjects, but in some subjects, some sub-cortical structures were > missing, for example, I can get R_Puta but L_Puta is missing. Sometimes > I run it again, then I can get another one. Is anybody has experience > about this and how to fix the problem? > Thank you in advanced. > Renxin > > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail.