Hi,
Have you checked whether there are any NaNs contained in the file?
You can check with fslmaths and the -nan or -nanm option.
Note that FSLView will not show NaNs, and instead shows them as zeros, so you cannot use FSLView to tell if they exist or not.
All the best,
Mark
On 7 Feb 2013, at 15:49, Matt Sutterer <[log in to unmask]> wrote:
> Hi,
>
> I'm trying to run smoothest on an unthresholded zstat map to obtain the DLH for cluster thresholding, but for some reason, I keep getting nan for the values. My colleague has no trouble running the same command on the same image and obtaining a value. My verbose output from smoothest is below. Is this something that you've encountered? I can't figure out why it works for her but not me?
>
> bash-3.2$ smoothest -z zstat1.nii.gz -m ../MNI152lin_T1_2mm_brain_mask.nii.gz -V
> verbose = 1
> help = 0
> dof = 100
> maskname = ../MNI152lin_T1_2mm_brain_mask.nii.gz
> residname = res4d
> zstatname = zstat1.nii.gz
> Reading mask....done
> mask:: Size = (91,109,91)
> mask:: ROI Size = (91,109,91)
> mask:: Dims = (2,2,2)
> mask:: Minimum and maximum intensities are: 0 and 1
> Reading datafile....done
> Data (residuals/zstat):: Size = (91,109,91,1)
> Data (residuals/zstat):: ROI Size = (91,109,91,1)
> Data (residuals/zstat):: Dims = (2,2,2,1)
> Data (residuals/zstat):: Minimum and maximum intensities are: -5.23127 and 7.25561
> Standardising....done
> Masked-in voxels = 258370
> SSminus[X] = nan, SSminus[Y] = nan, SSminus[Z] = nan, S2[X] = nan, S2[Y] = nan, S2[Z] = nan
> DLH nan voxels^-3 before correcting for temporal DOF
> FWHMx = nan voxels, FWHMy = nan voxels, FWHMz = nan voxels
> FWHMx = nan mm, FWHMy = nan mm, FWHMz = nan mm
> DLH nan voxels^-3
> VOLUME 258370 voxels
> RESELS nan voxels per resel
> DLH nan
> VOLUME 258370
> RESELS nan
>
> Thanks,
>
> Matt Sutterer
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