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Hi Mark, thank you! However, I think I am still missing something. In my case, the translation parameters in .par file does not seem to match that of the output matrix. See output below: >> mcflirt -in input.nii.gz -out input_mc.nii.gz -mats -plots -refvol 0 -rmsrel -rmsabs -report >> head -n 2 input_mc.nii.gz.par 0 -0 0 0 0 0 0 -5.36371e-05 0 -2.51772e-05 0.0353457 -0.0244103 >> avscale --allparams input_mc.nii.gz.mat/MAT_0001 Rotation & Translation Matrix: 1.000000 0.000000 0.000054 -0.003990 0.000000 1.000000 0.000000 0.035346 -0.000054 0.000000 1.000000 -0.018570 0.000000 0.000000 0.000000 1.000000 Rotation Angles (x,y,z) [rads] = 0.000000 -0.000054 0.000000 Translations (x,y,z) [mm] = -0.003990 0.035346 -0.018570 Thanks, Thomas On Tue, Nov 29, 2011 at 5:23 PM, Mark Jenkinson <[log in to unmask]> wrote: > Hi Thomas, > > The rotation matrix is formed as such: > R = Rx.Ry.Rz > and the translations are put in the 4th column. > This matrix multiplies the input coordinates > to form transformed coordinates in the reference > space. > > Given the amount of confusion about "radiological" > and "neurological" ordering, I'm not touching > "clockwise" with a barge-pole. You can take any > flirt or mcflirt matrix and get the equivalent > decomposition into parameters using: > avscale --allparams > > This way you can find yourself a "clockwise" > one (according to your definitions of this term) > and see what the angles are like! > > All the best, > Mark > > > On 29 Nov 2011, at 04:49, Thomas Yeo wrote: > >> Dear Mark (or other FSL experts), >> >> to clarify and expand on this question about in 2009 about the .par >> output of mcflirt, can I confirm that >> >> 1) rot_x is applied first, followed by rot_y, followed by rot_z, >> followed by the displacement (trans_x, trans_y, trans_z)? >> >> 2) And that the rot_x is rotation about x axis in the clockwise >> direction, etc. as suggested by Satra? >> >> Thanks, >> Thomas >> >> >> >> >> >> Hi, >> >> Not quite - they are the parameters you need to align with >> the reference volume (the middle of the timeseries in FSL). >> >> All the best, >> Mark >> >> >> On 9 Feb 2009, at 01:09, Satrajit Ghosh wrote: >> >>> Hi, >>> >>> Thanks. So am I correct in assuming the following: >>> >>> rot_x, rot_y, rot_z, trans_x, trans_y, trans_z >>> >>> rotations in radians and clockwise >>> translations in mm >>> >>> These are scan to scan changes rather than cumulative (like SPM). >>> >>> Cheers, >>> >>> Satra >>> >>> >>> On Sun, Feb 8, 2009 at 1:57 PM, Xinian Zuo <[log in to unmask]> >>> wrote: >>>> the first three columns are rot and last three are trans. >>>> >>> >> Hi, >> >> Is there a specification somewhere for the motion parameter estimates >> (par file) of mcflirt? I'm looking for information such as which >> fields are rotation, translation, what are the dimensions, is it scan >> to scan motion or cumulative, etc. >> >> Thanks, >> >> Satra >>