Dear Lucia and others

I think that Roberto pointed to a very important confound of VBM! 

The effect of iron and other microstructural tissue compartments on the contrast of an anatomical MRI image can be large. These can strongly confound your “volume” estimates in VBM (see, e.g., the very nice paper from the group of Bogdan Dragankski in Lausanne: http://www.sciencedirect.com/science/article/pii/S1053811914007861).

There are emerging techniques that can help to overcome these confounds – for a review see, e.g.:  http://www.ncbi.nlm.nih.gov/pubmed/26132532

Just my 2 cents.

Best
Siawoosh

Btw: I totally agree with Christian that the term “Gray Matter Concentration” can be very wrongly interpreted from a neurobiological point of view and thus should not be used for at all for VBM-estimated gray matter probability maps!

-- 
Dr. Siawoosh Mohammadi 
Institut für Systemische Neurowissenschaften (Department of Systems Neuroscience)
Universitätsklinikum Hamburg-Eppendorf (Medical Center Hamburg-Eppendorf)
Geb. W34 (S10)
Martinistraße 52
20246 Hamburg
Germany

Phone: +49-40-7410-59859
Fax:   +49-40-7410-59955
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> Gesendet: Donnerstag, 29. Oktober 2015 um 08:28 Uhr
> Von: "Christian Gaser" <[log in to unmask]>
> An: [log in to unmask]
> Betreff: Re: [SPM] Terminology debate: GM Volume vs Density
>
> Hello Lucia,
> 
> there are several reasons to not use the term density or concentration for modulated images:
> 1. Modulation means to correct (scale) the segmented images by the a amount of volume changes due to spatial normalization. The Jacobian determinant that is used for this step is a very common parameter in continuums mechanics to estimate local volume changes in fluids or gases. Therefore the Jacobian determinant expresses local volume changes (due to spatial normalization) and is used to scale your segmentations.
> 2. The term concentration or density is a rather misleading term for neurobiologists. VBM is not linked to that was is known as (cell) density in other fields that focus on microscopic changes.
> 3. Alternative segmentation approaches allow to model partial volume effects (PVE). That means that a voxel might contain different tissue types. The PVE allows to estimate the partial (fractional) volume of these tissue types in one voxel. A values of 0.8 in gray matter (GM) then means that this voxel contains of 80% GM and 20% of either WM or CSF (depending on the localization of that voxel). This is a partial volume and no probability as used in the non-PVE segmentation.
> 
> Personally, I always use the term volume for VBM...
> 
> Best,
> 
> Christian
> 
> On Wed, 28 Oct 2015 09:02:40 -0400, Lucía Vaquero <[log in to unmask]> wrote:
> 
> >Hello Marko,
> >
> >   Thank you so so much for your helpful reply! I agree with you in that
> >these terms are probably VBM-community specifc. But it is also because of
> >that that we wanted to keep that "classic" terminology, so everybody in
> >this community interested in our study can find and understand our
> >(potential) paper right away.
> >
> >I definitely think we should keep the term, even more seeing the match
> >between our innitial idea and what VBM experts use; but yes, we will add
> >more details in the methods regarding what do we mean by 'volume' and the
> >reason we're chosing this term.
> >
> >Thanks again for your time, your detailed and clear explanations and your
> >opinion on this toppic, really!
> >Kind regards,
> >
> >On 28 October 2015 at 04:20, Marko Wilke <[log in to unmask]>
> >wrote:
> >
> >> Hello Lucia,
> >>
> >> I would share your understanding and don't think that the reviewer is
> >> correct in stating that the term "volume" may only be used for manually
> >> segmented images. The difference between density and is introduced in the
> >> process of spatial normalization, and the volume changes occurring during
> >> this process are re-integrated into the data by modulation with the
> >> Jacobian.
> >>
> >> The sum of all voxel values, taking into account voxel sizes, is therefore
> >> the same in native space and normalized, modulated gray mater maps (with
> >> the exception of the special case of only correcting for the non-linear
> >> parts of spatial normalization, a specialty of Christian Gaser's vbm
> >> toolboxes).
> >>
> >> The terminology may be vbm-community specific, which may explain the
> >> reviewers opposition. I don't think it is wrong, though, so I think you
> >> should get away with clear definitions in the revised manuscript :)
> >>
> >> Cheers,
> >> Marko
> >>
> >> Luc ía Vaquero wrote:
> >>
> >>> Dear SPM and VBM experts,
> >>>
> >>> I'm addressing to you in order to try to solve an open debate we're
> >>> encountering during the review of a VBM study.
> >>>
> >>> My colleagues and I explained in the manuscript that, since we modulated
> >>> the images by their Jacobian determinants, we were looking at differences
> >>> in Grey Matter Volume or Amount of GM. However, one of the reviewers stated
> >>> that, even though one takes into account the Jacobian determinants, one's
> >>> still dealing with corrected probabilities after warping that are called
> >>> concentrations or GM density. So, he/she strongly recommends us to use GM
> >>> Density "because the term Volume can only be used when one does manual
> >>> segmentation of T1 images but not with VBM".
> >>>
> >>> That wasn't our understanding, we thought that GM Density is the term
> >>> when one doesn't do the modulation by the Jacobian determinants (leaving
> >>> this option by default in SPM) and Volume is the term when one applies such
> >>> modulation. All the information from older messages regarding this topic
> >>> and from previous reports and manuals (by Ashburner and other users of VBM)
> >>> seems to confirm our original concept, but we still have doubts and we
> >>> should be pretty sure if we're trying to keep our terminology despite what
> >>> the reviewer is asking us to do (change the term GM volume by GM density)...
> >>>
> >>> Thank you so much in advance for your time and help!
> >>> Best wishes,
> >>>
> >>>
> >>> Lucía Vaquero
> >>>
> >>> ------
> >>> Ph.D Student
> >>> Cognition and Brain Plasticity Unit
> >>> http://www.brainvitge.org/
> >>> University of Barcelona
> >>> Barcelona (Spain)
> >>> Tel: +34 93 402 10 38
> >>>
> >>>
> >>>
> >> --
> >> ____________________________________________________
> >> PD Dr. med. Marko Wilke
> >>  Facharzt für Kinder- und Jugendmedizin
> >>  Leiter, Experimentelle Pädiatrische Neurobildgebung
> >>  Universitäts-Kinderklinik
> >>  Abt. III (Neuropädiatrie)
> >>
> >> Marko Wilke, MD, PhD
> >>  Pediatrician
> >>  Head, Experimental Pediatric Neuroimaging
> >>  University Children's Hospital
> >>  Dept. III (Pediatric Neurology)
> >>
> >> Hoppe-Seyler-Str. 1
> >>  D - 72076 Tübingen, Germany
> >>  Tel. +49 7071 29-83416
> >>  Fax  +49 7071 29-5473
> >>  [log in to unmask]
> >>
> >>  http://www.medizin.uni-tuebingen.de/kinder/epn/
> >> ____________________________________________________
> >>
> >>
> >
> >
> >-- 
> >Lucía Vaquero
> >
> >Ph.D Student
> >*Cognition and Brain Plasticity Unit*
> >http://www.brainvitge.org/
> >University of Barcelona
> >Barcelona (Spain)
> >Tel: +34 93 402 10 38
> >
> >Currently on an internship @*Laboratory for Motor Control & Neural
> >Plasticity*
> >Concordia University
> >Montreal (Québec)
> >
> >https://www.researchgate.net/profile/Lucia_Vaquero
> >
> >------------------------------------------------------------------------------------------------------------------
> >
> >*“Lock up your libraries if you like; but there is no gate, no lock, no
> >bolt that you can set upon the freedom of my mind.” - *Virginia Woolf (“A
> >Room of One’s Own”)
> >
> >
> >*-----------------------------------------------------------------------------------------------------------------------------------------------*
> >
> ________________________________________
> 
> Christian Gaser, Ph.D.
> Associate Professor of Computational Neuroscience/Neuroimaging
> Structural Brain Mapping Group
> Departments of Psychiatry and Neurology
> Jena University Hospital
> Jahnstrasse 3, D-07743 Jena, Germany
> Tel: ++49-3641-934752	Fax:   ++49-3641-934755
> e-mail: [log in to unmask]
> http://www.neuro.uni-jena.de
>