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Hi, > Hi - the easy answer 9;-) is that we'll release a patch _very soon_ which > includes, amongst other things - these new Jeulich maps. > Cheers. OK, thanks. I'll wait for the patch. Nevertheless, I would argue that for reasons of transparency it would be still very nice to have the exact settings (or simply the transformation matrix). Best regards, Matthias > 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 >> > > > --------------------------------------------------------------------------- > 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) > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > --------------------------------------------------------------------------- >