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That work great, Gwenaelle. Thanks for your help! Ronan 2009/3/2 Gwenaëlle DOUAUD <[log in to unmask]> > Hi Ronan, > > if you have set up your results to be between 1.8 and 5 in the > brightness/contrast tool of fslview, then your colourbar between 1.8 (set up > again in the brightness tool of fslview, not with fslstat) and 5 (because > you've divided it by 20) should present the same range of colour... > > Cheers, > Gwenaelle > > > > --- En date de : Lun 2.3.09, Ronan Joseph Kelly <[log in to unmask]> a écrit : > > > De: Ronan Joseph Kelly <[log in to unmask]> > > Objet: Re: [FSL] Re : [FSL] Colour Bar Significance Values > > À: [log in to unmask] > > Date: Lundi 2 Mars 2009, 12h49 > > Hi Gwenaelle, > > > > Thanks for the email. Just one or two things I'm not > > too sure about. Say I > > divide the colourbar's intensity by 20 to produce a new > > colourbar with the > > range 0-5; how can I be certain that the significance value > > at a certain > > intensity in my tstat map is the same as the corresponding > > colour in the > > colour bar? It looks about right but I'm not sure.. > > Secondly, setting the > > min of my colourbar at 1.8, would that be done using the -l > > lower threshold > > option within fslstats? > > > > Thanks again, > > Ronan > > > > 2009/2/27 Gwenaëlle DOUAUD > > <[log in to unmask]> > > > > > Hi Ronan, > > > > > > the min value is a cutoff threshold in fslview, but > > the max one is not, it > > > just "saturates" the image (with my own > > non-English way of saying it!). If > > > the stats image you present are showing t-value say > > >1.8 and "saturated" at > > > 5, then all you need to do is something like: > > > fslmaths colourbar -div 20 new_colourbar and in > > fslview, set the min of > > > your new_colourbar at 1.8. You will then have a > > colourbar of min 1.8 and max > > > 5.. > > > Alternatively, you can just add/place the numbers > > "1.8" at the bottom of > > > your colourbar in your figure and "5" at the > > top, that will do! > > > > > > Cheers, > > > Gwenaelle > > > > > > > > > --- En date de : Ven 27.2.09, Ronan Joseph Kelly > > <[log in to unmask]> a écrit > > > : > > > > > > > De: Ronan Joseph Kelly <[log in to unmask]> > > > > Objet: [FSL] Colour Bar Significance Values > > > > À: [log in to unmask] > > > > Date: Vendredi 27 Février 2009, 17h43 > > > > Dear FSL experts, > > > > > > > > I have finished conducting a FSL-VBM analysis and > > have just > > > > produced my > > > > corrected tstat maps highlighting statistically > > significant > > > > voxel clusters > > > > between groups. The completed maps are produced > > with a > > > > colour gradient, > > > > highlighting the thresholded range of t values > > applied in > > > > the study > > > > (approximately t = 1.8 and above). My question > > concerns the > > > > use of colour > > > > bars to highlight different significance values > > in my maps. > > > > The 'colour > > > > significance bar' I have been trying to use > > is > > > > colourbar.nii.gz posted > > > > earlier this year in the FSL archives. However, > > the > > > > significance range in > > > > this is 0 - 100, so how do I threshold this to > > correspond > > > > to the values > > > > associated with the maps in my study? I've > > been trying > > > > to do it manually but > > > > no luck so far. Any ideas anyone? > > > > > > > > Many thanks, > > > > Ronan > > > > > > > > -- > > > > Ronan Kelly > > > > Neuroinflammatory Research Group > > > > Trinity College Institute of Neuroscience > > > > University of Dublin, Trinity College > > > > Dublin 2 > > > > Ireland > > > > > > > > > > > > > > > > > > > > > -- > > Ronan Kelly > > Neuroinflammatory Research Group > > Trinity College Institute of Neuroscience > > University of Dublin, Trinity College > > Dublin 2 > > Ireland > > > > > -- Ronan Kelly Neuroinflammatory Research Group Trinity College Institute of Neuroscience University of Dublin, Trinity College Dublin 2 Ireland