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I'm not actually sure what fslstats reports, but I suspect the results you are getting relate to how it handles NaNs. If SPM tries to generate a warped image and needs to sample a voxel that does not exist, then it will assign a value of NaN (not a number) if possible. This indicates that the value is totally unknown. Different software behaves differently with NaNs. For example, if a program to compute the mean of a series of numbers is presented with values of 1, NaN and 3, then the desired output is probably (1+3)/2 = 2. However, if it has not been coded to ignore NaNs, then it will give (1+NaN+3)/3 = NaN. Best regards, -John On Fri, 17 Aug 2018 at 02:06, Dianne Patterson <[log in to unmask]> wrote: > Dear SPM and FSL experts, > > I am comparing various options for normalization of lesioned brains across > ants, fsl and spm12, and I am confused by the following result: > > All of the warped images (w*) that spm12 generates are not interpretable > by fslstats (although you can view the image in fsleyes and see the brain > and range of values). What I mean by "not interpretable" is that > fslstats is reporting all the values in the image are nan. fslmaths also > cannot operate on these images as it thinks they are all nans. > > FSL does understand the values in the deformation field and the > segmentation images, just not the warped images...I have bolded the results > below for all the spm images... > > I have linked to a brain image: > https://arizona.box.com/s/8kxixwhpo97dmg7et96hw6llgyfbkbic so you can see > the problem: it can be viewed with fsleyes but fslstats and fslmaths think > it contains only nans. > > I am working with Matlab 2016b, spm12 and Mac OSX Sierra. Any insights > would be greatly appreciated! > Thanks, > > Dianne > > T1w.nii > 1.191157 622.975098 > T1w_brain.nii > 0.000000 438.224121 > *c1T1w_brain.nii* > *0.000000 0.993000* > *c2T1w_brain.nii* > *0.000000 0.993000* > *c3T1w_brain.nii* > *0.000000 0.953463* > *c4T1w_brain.nii* > *0.000000 0.463200* > *c5T1w_brain.nii* > *0.000000 1.000000* > lesionmask.nii > 0.000000 1.000000 > lesionmaskinv.nii > 0.000000 1.000000 > sub-001_T1w.nii > 1.191157 622.975098 > sub-001_T1w_brain.nii > 0.000000 438.224121 > sub-001_T1w_lesioninv.nii > 0.000000 1.000000 > sub-001_brain_mask.nii > 0.000000 1.000000 > *wT1w.nii* > *nan nan* > *wT1w_brain.nii* > *nan nan* > *wlesionmask.nii* > *nan nan* > *y_T1w_brain.nii* > *-86.839539 106.838730* > > > > > -- > Dianne Patterson, Ph.D. > Research Scientist > [log in to unmask] <[log in to unmask]> > or > [log in to unmask] > University of Arizona > Speech and Hearing Science 314 > 1131 E 2nd Street, Building #71 > (Just East of Harvill) > ============== > If you don't hear back from me (and you expected to), > I blame the University's new SPAM filter. > Please write to my gmail account. > ============== > Antipiphany: That moment when you realize how little you actually know > ============== > -- Prof John Ashburner Professor of Imaging Science UCL Institute of Neurology Queen Square Wellcome Trust Centre for Neuroimaging University College London 12 Queen Square, London, WC1N 3BG E: [log in to unmask] T: +44 (0)20 3448 4365 http://www.fil.ion.ucl.ac.uk/