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Hi, That's a typo - thanks for letting me know. It is now fixed. All the best, Mark From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of "Huang Su (I2R)" <[log in to unmask]<mailto:[log in to unmask]>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> Date: Monday, 24 August 2015 10:33 To: "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>> Subject: Re: [FSL] Skew values in avscale output Hi Mark, Thanks for your explanation. It is clear to me now. P.S. On the reference web page, the illustration of the skew_mat should be an upper triangle matrix, isn't it? Then the element at (3,2) position should be 0. Is it a typo, or I didn't understand correctly. Best regards, Sullivan ________________________________________ From: FSL - FMRIB's Software Library [[log in to unmask]<mailto:[log in to unmask]>] on behalf of Mark Jenkinson [[log in to unmask]<mailto:[log in to unmask]>] Sent: Monday, August 24, 2015 4:24 PM To: [log in to unmask]<mailto:[log in to unmask]> Subject: Re: [FSL] Skew values in avscale output Hi, You are right that skew and shear are just different words for the same thing. There are only 3 *independent* parameters that describe pure shear (or skew) in 3D. For instance, combining +/-90 rotations with any of the upper triangular elements generates matrices that contain these values in the lower triangular part. Hence, when taken in context of the full set of other DOF in the transformation (particularly rotations) it is only necessary to have 3 shear terms (one for the x-y plane, one for the x-z plane and one for the y-z plane). Whether they are parameterised by upper or lower triangular elements is a matter of choice/convention. In FLIRT the upper triangular elements are used, which is our convention. For more information about the FLIRT parameters and conventions see: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/FAQ#What_is_the_format_of_the_matrix_used_by_FLIRT.2C_and_how_does_it_relate_to_the_transformation_parameters.3F All the best, Mark P.S. Also note that your matrix, parameterised by a-f, would also describe matrices that are normally considered as rotations plus scalings (as the axes maintain their 90 degree orthogonality, which is not true for shears). For example, a=0.1, c=-0.1, and all others set to zero, would describe a small rotation plus some additional, uniform scaling. So this parameterisation is not just more than is necessary for describing shears generally, but actually describes more than just pure shears. From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]><mailto:[log in to unmask]>> on behalf of Sullivan Huang <[log in to unmask]<mailto:[log in to unmask]><mailto:[log in to unmask]>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]><mailto:[log in to unmask]>> Date: Monday, 24 August 2015 01:51 To: "[log in to unmask]<mailto:[log in to unmask]><mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]><mailto:[log in to unmask]>> Subject: [FSL] Skew values in avscale output Hi all, avscale outputs 3 skew values. To my understanding, skew is equivalent to shear. While shear matrix typically is | 1 a b 0 | | c 1 d 0 | | e f 1 0 | | 0 0 0 1 | which has 6 parameters. How does the 3 skew values of avscale output corresponding to the 6 parameters? Thanks for any help. Regards, Huang Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."