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Hi - in general it is good to model all the conditions (including fixation) even if you don't intend to use all the resulting EVs, so that you minimise the unmodelled noise in the model fitting. Cheers. On 13 Jul 2007, at 19:21, Heather Cogswell wrote: > Hi Steve, > > I am very worried that the negative PEs may be due to an error on > my part in the > way I modeled the experiment conditions in Feat. There were 18 > conditions during > the experiment plus one condition for the fixation. I am only > interested in 6 of > the 18 conditions in the experiment, so I only had 6 EVs in my Feat > design plus > one EV for the fixation. I did not include the other conditions in > the design. > Does this mean that my PE1 is the difference between EV1 and the > conditions > that I did not include in the design file? > > Should I add all the other conditions to the Feat model, and remove > the fixation > EV to solve this? > > thanks, > Heather > > > > > Quoting Steve Smith <[log in to unmask]>: > >> HI - maybe it just means that these images had no positive values >> within the mask? >> Cheers. >> >> >> >> On 13 Jul 2007, at 16:56, Heather Cogswell wrote: >> >>> Hi Steve, >>> Thank you for your prompt reply! >>> >>> I used the same binary mask for six contrasts on one subject. >>> The position of >>> the max voxel for some of the contrasts is (0 0 0 ) which does >>> not make sense. >>> I was wondering why this is happening? Below is a sample >>> featquery with the >>> above problem (i.e. pe2 and pe4) >>> >>> >>> 1 stats/pe1 5 0.00 0.31 0.59 0.62 0.89 0.89 23 37 7 25.32 1.38 >>> -15.90 >>> 1 stats/pe2 5 -0.74 -0.74 -0.62 -0.70 -0.39 0.00 0 0 0 103.93 >>> -112.31 -36.09 >>> 1 stats/pe3 5 -0.35 -0.35 -0.07 -0.17 0.32 0.32 24 36 7 22.06 >>> -1.59 -15.59 >>> 1 stats/pe4 5 -2.54 -2.54 -1.94 -1.92 -1.46 0.00 0 0 0 103.93 >>> -112.31 -36.09 >>> 1 stats/pe5 5 -0.13 -0.13 0.52 0.59 0.90 0.90 24 36 7 22.06 >>> -1.59 -15.59 >>> 1 stats/pe6 5 -0.65 -0.65 -0.25 -0.45 0.64 0.64 24 37 7 22.03 >>> 1.34 -16.02 >>> >>> Many thanks, >>> Heather >>> >>> >>> >>> >>> Quoting Steve Smith <[log in to unmask]>: >>> >>>> Hi, >>>> >>>> On 12 Jul 2007, at 16:30, Heather Cogswell wrote: >>>> >>>>> Dear FSL users, >>>>> >>>>> I'm an FSL newbie, so thanks in advance for your help! >>>>> >>>>> How can I make a mask from a 3rd level activation? I tried >>>>> avwroi but it >>>>> just creates the mask of the specific voxels that I >>>>> input . . . I want to >>>>> create a mask of the chosen voxels overlaid on the entire brain. >>>> >>>> I'm not sure what you're asking - you should probably take the >>>> appropriate thresh_zstat image from inside the appropriate >>>> something.gfeat/cope??.feat directory and maybe binarise this >>>> with avwmaths++ >>>> >>>>> For Featquery analysis I can choose "stats/pe" or "stats/ >>>>> cope". Which one >>>>> should I use for ROI analysis? >>>> >>>> It's up to you. If this isn't clear then you should probably >>>> read the FEAT manual carefully, including the intro to GLM etc >>>> stuff in it - hopfully then it will be clear which is what you >>>> want. >>>> >>>> Cheers, Steve. >>>> >>>> >>>> >>>>> >>>>> >>>>> Thanks, >>>>> Heather >>>> >>>> >>>> ------------------------------------------------------------------- >>>> -- --- --- >>>> 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 >>>> ------------------------------------------------------------------- >>>> -- --- --- >>>> >> >> >> --------------------------------------------------------------------- >> --- --- >> 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 >> --------------------------------------------------------------------- >> --- --- >> ------------------------------------------------------------------------ --- 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 ------------------------------------------------------------------------ ---