I've taken a quick look at your job file, and think this question may be for
Christian Gaser.
Best regards,
-John
On Wednesday 06 May 2009 22:31, Neil Chatterjee wrote:
> Thank you for your quick reply!
>
> I am using SPM5 on a Windows XP x64 installation of Matlab R2008b.
>
> I kept the options at defaults except for 'Set origin'. I've attached a
> copy of a template script used to generate these images.
>
> They are m0 instead of m because the images are modulated only by the
> non-linear compression map. To quote the tooltip: "Modulated images
> can be optionally saved by correcting for non-linear warping only
> ... I recommend this option if your hypothesis is about effects of
> relative volumes which are corrected for different brain sizes. This
> is a widely used hypothesis and should fit to most data...These
> modulated images are indicated by 'm0' instead of 'm'."
>
> Regards,
> Neil
>
> John Ashburner wrote:
> > My best guess is that the modulated images are stored as some form of
> > integer datatype, with a scalefactor. To help me narrow down the cause
> > of the problem, I need a few more details before I try to figure out the
> > cause.
> >
> > Which version of SPM are you using?
> > Which options did you use to generate the modulated images?
> > Why are they called m0wc1*.nii instead of mwc1*.nii?
> >
> > Best regards,
> > -John
> >
> > On Tuesday 05 May 2009 21:05, Neil Chatterjee wrote:
> >> Dear SPMers,
> >>
> >> I came across several oddities in my m0wc1*.nii (modulated, normalized,
> >> gray matter) images yesterday, and I am hoping someone here can shed
> >> some light on the situation. Apologies for the length of this
> >> correspondence, but I wanted to be precise in explaining the problem
> >> observed.
> >>
> >> Anyways, looking at a typical m0wc1*.nii image, the voxel values have
> >> the following strange properties:
> >>
> >> 1) There are no voxels with a value greater than 1
> >> 2) There are ~580,000 voxels with a value of exactly 1. Actually, they
> >> all have a value of exactly 1.000000059138983, which in itself is kind
> >> of strange. 3) Of the non-zero valued voxels in the m0wc1*.nii image,
> >> 42.4% of them are exactly (to double precision) the same as in the
> >> wc1*.nii images.
> >>
> >> In a previous thread, Dr. Ashburner said that
> >>
> >>> The contents of a modulated image are a voxel compression map
> >>> multiplied
> >>
> >> by tissue belonging
> >>
> >>> probabilities (which range between zero and one)
> >>> ...
> >>> The total volume of grey matter in the original image can be
> >>> determined by summing the voxels in the modulated, spatially
> >>> normalised image and multiplying by the voxel volume (product of voxel
> >>> size).
> >>
> >> That the total volume of gray matter in the original image can be
> >> determined by integration implies conservation of probability of gray
> >> matter. It follows that the voxel compression map would have values >1
> >> in areas where there has been positive compression (shrinking) and
> >> values <1 in areas where there has been negative compression
> >> (expansion). With this in mind, the properties described above lead me
> >> to the following conclusions:
> >>
> >> A) There are no voxels with high probability (p~1.0) of being gray
> >> matter that were positively compressed (shrunk) in normalizing, else
> >> there would exist modulated voxels with value > 1.
> >> B) There exist several voxels that either i) had a gray matter
> >> probability of exactly 1 and were not compressed even one iota or ii)
> >> were compressed in exact (to double precision!) proportion to their
> >> uncertainty of being gray matter. Else there would not exist modulated
> >> voxels with value = 1 exactly C) 42.4% of probable gray matter voxels
> >> neither shrunk nor expanded in the process of morphing to standard
> >> space.
> >>
> >> I just can't wrap my head around any of those conclusions. I feel like
> >> either I'm totally misunderstanding what happens with modulation or
> >> something is very very wrong with my images. I understand that the
> >> non-linear only modulation (m0 instead of m) changes things, but
> >> substituting "non-linear compression" for "compression" above does not
> >> make the observations any less strange. If any guru out there can make
> >> sense of all this, it would be much appreciated.
> >>
> >> Regards,
> >> Neil
> >>
> >> Neil Chatterjee
> >> Research Assistant
> >> Stanford Systems Neuroscience and Pain Lab
> >> 650-724-0522
> >> [log in to unmask]
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