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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