Ged,
the "anatomical MNI space" is indeed sort of a hybrid generated from two diverging needs:
i) to be as compatible as possible with the MNI / ICBM reference space, so that functional imaging data can be correlated with anatomical information without the need of extensive (re-) normalisation
ii) to have anatomical information described on in individual atlas brain, which conforms to stereotaxic definitions, in particular in terms of the coordinate origin.
The solution was to choose the MNI single subject brain (colin27), which is well aligned with the MNI / ICBM multi-subject templates, as the reference brain. However, the location of the MNI sapce origin does not match the AC in this particular brain. Hence we introduced the translation described in Rick's email, which renders the template anatomically "correct" but still allows for an easy use in the context of SPM (and other packages using the MNI / ICBM reference space.
Rick,
Phillip described the solution to your problem (i.e. reslicing). Two things to be aware of:
1) Make sure MRIcro get the left-right conventions correctly (as a tip: The posterior end of the interhemispheric fissure of the Colin27 brain has to slanted to the right)
2) Remember, that a shift of the origin backwards and up (to convert anatomical MNI into proper MNI) corresponds to shifting the image foreward and down.
Best wishes
Simon
----- Original Message -----
From: Rick Helmich <[log in to unmask]>
Date: Wednesday, December 20, 2006 8:35 pm
Subject: Re: [SPM] Anatomy toolbox: reorient colin27 to MNI
> > I'm very confused by this... I thought SPM results were in MNI
> space.
> > As far as I understand the various templates, from e.g.
> > http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach
> > SPM's templates are in the space of MNI305 and ICBM152. Can you
> give any
> > more information/references about the shift you discuss?
>
> > Thanks,
> > Ged.
>
> Dear Ged,
>
> Don't worry about spm: the templates are indeed in MNI space.
> However, as I
> understand it the Anatomy Toolbox works with an adapted MNI space,
> which
> they name "anatomical MNI space" (see below for the passage where
> they
> explain that, in Eickhoff et al. NIMG 2005). That was meant to
> keep the AC
> at [0 0 0], which is not the case in he "original" MNI space. It
> does mean,
> however, that the very nice skull-stripped template (colin27) they
> use is
> also is this "anatomical" MNI space. That does not fit with the
> "original"
> MNI space as employed by SPM...
>
> Greetings, Rick
>
> Eickhoff et al. NIMG 2005:
>
> "The probabilistic maps are located in the space of the T1
> weighted MNI
> single subject template (Collins et al., 1994, Evans et al., 1992
> and
> Holmes et al., 1998). The origin of the MNI space is located 4 mm
> more
> caudally (y axis) and 5 mm more dorsally (z axis) than the
> intersection
> between the AC and the interhemispheric fissure in this specific
> brain. To
> keep the AC as the anatomical reference of the coordinate system,
> the
> origin of the probabilistic maps was corrected for this
> displacement. The
> correction results in the so called “anatomical MNI space,” which
> differs
> from the original MNI space by an affine translation along the y
> and z axes
> of 4 and 5 mm, respectively. When using these maps for
> structure–function
> analysis, the user is prompted, whether the functional data have
> been
> normalized to the templates in standard MNI space as provided by
> SPM2 or
> the corresponding templates in anatomical MNI space as used by the
> SPM
> Anatomy toolbox. If the functional data have been normalized into
> the
> standard MNI space, the SPM Anatomy toolbox automatically applies
> the
> linear correction to the anatomical MNI space. All locations are
> then
> reported both in standard and anatomical MNI coordinates."
>
>
-----------------------------------------
Simon Eickhoff
Institut for Medicine (IME); Research Center Jülich
Leo-Brandt-Str. 5; 52425 Juelich, Germany
Phone + 49 2461-61-5219 / Fax + 49 2461-61-2820
e-mail: [log in to unmask] / [log in to unmask]
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