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Dear Ayelet, Not sure I'm following you here... >Still what if I want to transform coordinates in the original/template space now, which one? Original OR template? >back to the original space without generating the roi.img. ? If you don't have a roi.img, what would you transform? >What transformation should I apply, how should I compensate for the different origins/ dimensions? Let's assume you're talking about a transformation from template/MNI/ICBM152 space back to your original, and you have previously normalised original.img, so you've got woriginal.img and original_sn.mat. You go to the deformation toolbox, select "deformation from sn.mat", and choose your original_sn.mat. After a minute or so, you get a y_original.img. Now, in the Def. toolbox, you choose "Invert deformations", choose y_original.img, and the image to base your inverses on will be the original.img. Some five mins later, you've got an iy_original.img. Now, in the Def. toolbox, you choose "Apply deformations", 1 subject, select the iy* deformation field, and the image(s) to warp are the image(s), _in_template/MNI/ICBM152_space_, that you want to warp back to your original.img. You don't have to take the different matrix dimensions / absolute sizes / origins into account because all that information is in the transformations you're inverting. It's all very convenient, really! >Many thanks for your help, Hope this helps, Alexander Ayelet -----Original Message----- From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Hammers, Alexander Sent: Sunday, May 08, 2005 11:19 AM To: [log in to unmask] Subject: Re: [SPM] deformation toolbox: get the roi in a normalized space corresponding to original Dear Ayelet, Fortunately this is a lot easier than you thought, and you don't need the Deformation toolbox. You just select Normalise, write normalised only, select your original_sn.mat, image to write: roi.img. This is assuming your roi.img and original.img are in the same space (Even though I think SPM would be able to cope even with different voxel sizes as long as the origins are correct). Note, however, that you probably need your wroi.img (in MNI/ICBM template space) as a binary image, or at least with all voxels unequivocally assigned to allow subsequent sampling. You will therefore need to change the Normalisation defaults (via the Defaults button) to Nearest Neighbour interpolation. Enjoy, Alexander -----Original Message----- From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]On Behalf Of Ayelet Akselrod-ballin Sent: 07 May 2005 18:20 To: [log in to unmask] Subject: [SPM] deformation toolbox: get the roi in a normalized space corresponding to original Dear list, I'm a little confused, about how to get an roi in the normalized space corresponding to the original image normalized. After normalizing my original.img to the T1 template space, I want to apply the same transformation to a corresponding roi.img to get the roi in the normalized space. Should I use the deformation tool box as follows: 1)Get the Deformation from sn.mat 2)Apply the y.img deformation to the roi.img Or am I supposed to Invert the y *.img deformation and apply the iy *.img deformation Also, is this all there is to applying both the linear and non-linear transformation components, or should I keep in mind anything else (e.g initial orientation, dimensions differences between the original image and template) your advice will be appreciated a lot, Many thanks, Ayelet