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I'm not really sure. I guess it depends on the max and min values in the images, which would be used to determine the histogram binning. Best regards, -John On 15 May 2014 15:09, Dorian P. <[log in to unmask]> wrote: > Dr. Ashburner, > > I am trying to understand why the joint histogram starts at different > positions on the X and Y axes. The X axis seem to have the majority of the > voxels starting around bin 50 while the Y axis starts correctly at bin 1. > Is there an explanation for this? > > Thank you. > > > 2014-05-14 14:36 GMT-04:00 John Ashburner <[log in to unmask]>: > > Perhaps it's just in the display. If I remember correctly, the >> coregistration displays log(H+1), rather than H. >> >> Best regards, >> -John >> >> >> >> On 14 May 2014 18:38, Dorian P. <[log in to unmask]> wrote: >> >>> Thank you Dr. Ashburner, >>> >>> I managed to get colored histogram following your advice (below an >>> example). The result is a little different from what spm_hist2 produces, >>> but I guess this has to do with differences in calculation algorithm. >>> >>> Thank you. >>> Dorian >>> TJU >>> >>> [image: Immagine in linea 1] >>> >>> >>> >>> 2014-05-13 16:02 GMT-04:00 John Ashburner <[log in to unmask]>: >>> >>> I won't help with all the coding, but I could give you a few pointers. >>>> You can read images by: >>>> >>>> P=spm_select(Inf,'nifti'); >>>> Nii=nifti(P); >>>> >>>> x=Nii(1).dat(:); >>>> y=Nii(2).dat(:); >>>> >>>> If you can convert x and y into integer values, ranging from 1..Nx and >>>> 1..Ny then you can use MATLAB's sparse function to create the joint >>>> histogram (providing the images are the same size and are in alignment >>>> voxel-for-voxel). >>>> >>>> H = full(sparse(x,y,1,Nx,Ny)); >>>> >>>> If you have a mask (say a variable z) of ones and zeros, you can get >>>> the values within the mask by >>>> >>>> xmask = x(logical(z)); >>>> ymask = y(logical(z)); >>>> >>>> You can then generate a joint histogram from this subset of voxels. >>>> >>>> If you want to display something in colour, then you'll need to rescale >>>> the histograms to have values between 0 and 1, and combine three such >>>> images as rgb = cat(3,Hr,Hg,Hb), before using image(rgb). >>>> >>>> Best regards, >>>> -John >>>> >>>> >>>> >>>> >>>> >>>> On 13 May 2014 19:42, Dorian P. <[log in to unmask]> wrote: >>>> >>>>> Hi SPM list, >>>>> >>>>> I am trying to plot a joint histogram of two images where voxels >>>>> within a mask (third file) are colored differently. The function >>>>> spm_hist2.m seem to be compiled and therefore not editable. >>>>> >>>>> Anybody can help with how to change the colors of specific dots in a >>>>> joint histogram? >>>>> >>>>> I am using SPM8 on Windows Matlab 2012b. >>>>> >>>>> Thank you. >>>>> Dorian >>>>> TJU >>>>> >>>> >>>> >>> >> >