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 LISTSERV Archives SPM Home SPM July 2008

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Re: Reorientation of T1 images

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Fri, 25 Jul 2008 11:42:33 +0100

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 This depends on the order that you want to perform the operations. In most cases, it can be easier to use the Display button to try different operations by trial and error. Once you have a suitable set of parameters, then clicking on the "Reorient images" button will allow you to select which images you plan to reorient. Once you have the correct values, then you can put them in a vector and compute a matrix that can be used to reorient your images, like so: p = [0 0 0 -pi/2 pi/2 0 1 1 1 0 0 0]; M = spm_matrix(p) It is worth noting that the order of rotations matters. For example, the two following matrices (M1 and M2) differ: r1 = [0 0 0 -pi/2 0 0 1 1 1 0 0 0]; r2 = [0 0 0 0 pi/2 0 1 1 1 0 0 0]; M1 = spm_matrix(r1)*spm_matrix(r2) M2 = spm_matrix(r2)*spm_matrix(r1) Another way to do it is to figure out which directions you want to swap around, and simply enter 1s and -1s in the appropriate places. However, if you do this, it is a good idea to check out whether it is going to flip your data by: det(M) This indicates the relative volume change incurred by the transform, and a negative value would indicate a flip. Best regards, -John On Friday 25 July 2008 08:45, Armin Blickenstorfer wrote: > Dear community > > I would like to reorient the T1 images of my subjects with following > rotations: -pi/2 along pitch axis and pi/2 along roll axis > Attached you see the reorientation matrix displying a L-R flip. How do I > change the parameters to get the reorientation I would like to achieve? > > Thank you > > Armin Blickenstorfer > PhD Student > > Institute of Neuroradiology > University Hopital Zurich > Frauenklinikstrasse 10 > CH - 8091 Zurich > > Tel: +41 (0) 44 255 5603 > Fax: +41 (0) 44 255 4504

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