> They where normalized with 4th degree B-Spline.
How were the scalefactors in the original lesion map images set, and what
value was assigned to the lesion in these data? If a value of 1 was assigned
to the lesion (before accounting for the scalefactor), then the resliced data
would require values between 0 and 1 to represent the intensities. These
would be rounded to the closest value (ie zero or one).
In previous versions (before these updates), SPM automatically rescaled the
intensities to the max and min values in the volume and determined a suitable
scalefactor. This strategy caused problems for 4D data (see emails on list),
so was changed. The current strategy is now to preserve the original
scalefactor.
If you have an 8 bit lesion mask, then I would suggest setting the lesion
voxels to a value of 255, and using a scalefactor of 1/255.
> >> we just wanted to note that with the updates for SPM 5 from 18th january
> >> the images of lesions appeared only in binary form after normalization
> >> (0 or 1 values) when we opened them in MRIcron. And even when displaying
> >> them in SPM 5 the intensity values had a lower range than before
> >> (especially when using NN interpolation) But after normalization you
> >> expect them to have values ranging from 0 to 1.
> >
> > I'm not sure what happened here. Were the spatially normalised versions
> > created with NN interpolation?
> >
> >> Additionally after installing the updates the header information
> >> displayed in MRIcron when we open the normalized files occurs as (nifti
> >> embedded) even if the files were of header+img type before. With the old
> >> version no problem occurs. We wonder if there has be a change in the
> >> format of the output files which could be in line with the new updates?
> >
> > The updates shouldn't have changed anything here. NIfTI can be either
> > .nii or .img+.hdr. See http://nifti.nimh.nih.gov/nifti-1
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