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If you download and use my peak_nii toolbox ( www.martinos.org/~mclaren/ftp/Utilities_DGM), then you can get all the peaks within this cluster (rather than just the top 3). Use the same thresholds as you did in SPM. No, you can't do waht you are asking. Small volume correction/masking must be done with an orthogonal contrast, not the contrast you are using. However, you can get all the peaks from my program. This might help you get around the issue. I'm not sure what you mean the the second part of your analysis. You have to be careful about doing analysis on regions defined from your contrast as you get into issues of circularity (aka double dipping). 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 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, Jan 31, 2012 at 6:41 AM, Josh <[log in to unmask]> wrote: > Dear clever people, > > Background: > I am conducting a study where 10 participants have been asked to perform a > simple tone-paced joystick movement task with their eyes closed. It is an > epoch-related the design, where the movements are performed during the six > 30 second movement epochs per scan, each subject having two scans during > two different conditions (1 and 2). I have created a T-contrast showing the > main effect of movement regardless of condition, and at p<0.05 (FDR > correction), I have defined a motor network associated with the task. My > aim is to now do small volume analysis of each of the regions defined by my > motor network, on contrasts examining the difference in scan conditions (T > contrasts 1>2, and 2>1). > > Unfortunately, in the main effect of movement contrast, I have one large > cluster (3213 voxels) which spans a number of motor areas associated with > the task (M1, S1, lateral premotor area, superior parietal lobule and > intra-parietal sulcal cortex), which SPM has given me peaks in just 3 of > these areas. The other regions are also clearly active, but in order to > carry out my restricted volume analysis, I need to determine the sub-peaks > within the large cluster. > > Question: > Is it possible, and is it justifiable, to create a mask of the large > cluster and then perform a restricted volume analysis on the main effect of > movement contrast to get SPM to give me the sub-peaks, and then use these > peaks in the second part of my analysis? >