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SPM  May 2009

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Subject:

Re: strangeness in m0wc1*.nii : possible VBM bug?

From:

Christian Gaser <[log in to unmask]>

Reply-To:

Christian Gaser <[log in to unmask]>

Date:

Fri, 8 May 2009 21:43:36 +0100

Content-Type:

text/plain

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text/plain (130 lines)

Hi Neil,

to isolate to problem I need more information:
- Is this problem also occuring for unmodulated and modulated images
(including the affine component)?
- Please can you send me the raw T1-image and the *seg.mat file to my mail
address.

Regards,

Christian

____________________________________________________________________________

Christian Gaser, Ph.D.
Assistant Professor of Computational Neuroscience
Department of Psychiatry
Friedrich-Schiller-University of Jena
Jahnstrasse 3, D-07743 Jena, Germany
Tel: ++49-3641-934752	Fax:   ++49-3641-934755
e-mail: [log in to unmask]
http://dbm.neuro.uni-jena.de


On Wed, 6 May 2009 14:31:55 -0700, Neil Chatterjee <[log in to unmask]> 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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