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Hi On 12 Sep 2011, at 16:32, David Soto wrote: > Hello, > > > In order to derive the temporal course of a ROI I follow these steps > > 1) Draw an spherical ROI using fslmaths, > > (e.g.) > fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz -mul 0 -add 1 -roi 32 1 68 1 29 1 0 1 -kernel sphere 3 -fmean rOFC -odt float > > 2) Use featquery to derive the temporal course for each individual subject in the relevant COPE > by using the mask output in step 1)using the output > In featquery I select - DO NOT binarise mask (allow weighting)...... > > the thing is that if I don't select the DO NOT Binarise then the temporal course file contains only zeros is this just because the values in your mask are too low? Cheers > > is this OK? > > On a related note, I also use featquery to derive the % signal change for each individual subject > based on the cluster_mask_zstat at the highest level....I think that selecting DO NOT Binarise mask may be problematic here > becos the cluster_mask_zstat's variation in the z values will be weighted in the extraction of the % signal change for each individual subject..which does not seem right. > > I would appreciate to hear from you what is the role of using DO NOT binarise mask (allow weighting) and when should be used and when not- which by the way in one of the FSL feat practicals it is said to use it! > > http://www.fmrib.ox.ac.uk/fslcourse/lectures/practicals/feat1/index.htm > > Cheers, David > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------