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Hi Jim, Can you multiply your image by the binary mask (avwmaths in.image -mult bin.mask out.image), then run your feat program on the new 'roi' image? -Ryan On Jan 8 2007, James N. Porter wrote: >Hello Doug- > >Well, I suppose the problem is I'm unsure of the formula used to >calculate z-stats from intensity values. Since FEAT doesn't know what my >ROIs are, I assume that my N-size/population is all the voxels in the >brain, but is mu the mean value of all brain voxels, or does FEAT use >info from FAST to know when a voxel is labeled as grey or white matter >and use the appropriate mean greyscale value? > >Basically, my issue is that when I run FEAT and take a look at, for >example, cluster_zstat1.html, then I get a great table of clusters and >voxel counts and max z-stats. However, these clusters are distributed >across the brain, and I want to know specifically what are the max >z-stats for each individual in a particular predefined cortical region. >Yes, the table includes xyz coordinates and I could locate each cluster >individually, but that's not a feasible option across dozens of subjects >with multiple analyses. So, in an attempt to streamline things I've run >reg-feat2anat and associated processes to create binary masks of >particular cortical regions, and hoped to obtain the same cluster list & >local maxima tables found in cluster_zstat1.html, but constrained by my >ROIs via masking in Featquery or pulling rows out of mri_segstats. > >I suppose if I knew what FEAT was using as mu, sigma, and N, then I >could use the max intensity value output to calculate my own max z-scores. > >Thanks for your assistance. > >Jim Porter >TRiCAM Lab Coordinator >Elliott Hall N437 >612.624.3892 >www.psych.umn.edu/research/tricam > > > >Doug Greve wrote: >> Hi James, >> >> mri_segstats will include the max for each segmentation. Is this not >> what you want? Or is it a format issue? >> >> doug >> >> >> >> >> >> On Sat, 6 Jan 2007, James Porter wrote: >> >>> Hello- >>> >>> I'm hoping to obtain outputs of activation z-statistics by ROI. I've >>> used >>> FreeSurfer to create ROI masks for all of my subjects, and run >>> Featquery to >>> obtain information about the ROI. However, I was disappointed to see the >>> output options do not give me the ability to generate tables of max >>> z-stats, >>> as the first-level FEAT output does. >>> >>> Likewise, I've used FreeSurfer's mri_segstats program to create stats >>> tables >>> delineated by ROI, but it gives similar output as Featquery. >>> >>> What path should I have gone down to obtain z-stat tables within masked >>> ROIs? My first thought right now is to run a first-level FEAT >>> analysis on >>> the masked functional volumes, but I'm willing to bet that you all >>> have a >>> better solution. >>> >>> Thanks for your help. >>> >>> >> > -- ========================================================== Note: The materials in this e-mail are private and may contain Protected Health Information. If you are not the intended recipient be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender. ==============================================================