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My peak_nii tool can be scripted. It saves out the thresholded images. It also saves out the clusters and peaks and subsequently labels all the peaks as well. In the next release, it will also provide the corrected statistics (FWE/FDR) at both the voxel and cluster level. http://www.martinos.org/~mclaren/Utilities_DGM Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Tue, Mar 13, 2012 at 11:24 AM, Aaron Oliver-Taylor < [log in to unmask]> wrote: > Hello, > > I was wondering if anyone could tell me how to > batch/automatically/programatically save the activation maps for each > contrast during standard fMRI analysis. This would manually be achieved by > going to the results window, selecting spm.mat, selecting the contrast, > clicking save and entering a filename. I have a batch job which handles > all of the other aspects of processing, and is similar to the batch job > example in the spm 8 manual. > > Many thanks, > > Aaron > __________________________________________ > Aaron Oliver-Taylor > Ph.D Student > The Advanced Magnetic Resonance Imaging Group > Department of Medical Physics and Bioengineering > University College London > [log in to unmask] > >