Hi - the easy answer 9;-) is that we'll release a patch _very soon_
which includes, amongst other things - these new Jeulich maps.
Cheers.
On 17 Apr 2009, at 05:37, Matthias Ekman wrote:
> Hi,
>
> This question concerns the topic of how the standard FSL probability
> map
> transformation works. In other words: how do you transform the JHU
> probability maps (which are in colin27 (1mm) space) to the MNI152
> (2mm) brain?
>
> I need the probability map of V4 which is available since December
> 2008 from
> the SPM Anatomy Toolbox (www.fz-juelich.de/inm/spm_anatomy_toolbox),
> but not
> yet integrated in FSLVIEW.
>
> I tried the following procedure (which failed)
>
> 1) Transformation of colin27 template to the MNI152_T1_2mm_brain
> template
> 2) apply the resulting transformation matrix to the V4 probability map
>
> (I also tried to transform colin27 first to MNI152_T1_1mm_brain and
> afterwards to MNI152_T1_2mm_brain, concatenate the transformation
> matrices
> and apply it to the V4 probability map... with the same result)
>
> My Settings:
> -cost corratio -dof 7 -searchrx -180 180 -searchry -180 180 -
> searchrz -180
> 180 -interp trilinear
>
> To check this procedure I repeated these steps for the probability
> map of V5
> and compared the result to the V5 map included in FSLVIEW.
> The result looks quite different.
>
> In the manual (http://www.fmrib.ox.ac.uk/fsl/data/atlas-descriptions.html
> ),
> it says, that "The histological volumes of these brains were 3D
> reconstructed and spatially normalised into the space of the MNI
> single
> subject template to create a probabilistic map of each area. For the
> FSL
> version of this atlas, these probabilistic maps were then linearly
> transformed into MNI152 space"
>
> So, I also tried the following steps
>
> 1) Transformation of colin27 to the MNI single subject brain
> 2) Transformation of MNI single subject brain to the
> MNI152_T1_2mm_brain
> template
> 3) concatenate the transformation matrices
> 4) applied it to the V4 probability map
>
> repeating the same steps with V5 to check the result... and this
> also fails
> to reproduce the FSL V5 map.
>
>
> Could you please describe your procedure for the probability
> transformation
> and the exact settings you are using?
>
>
> Best regards,
> Matthias
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
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