Hi Pradeep, sorry for the delay -- busy for the holidays. Anyhow, something looks very strange there. With the matrix you're listing, that determinant doesn't make any sense. Can you post a little more context about what you're trying to do? Also, what version of FSL are you using? With that matrix, I get completely different output:
fsl5.0-avscale --allparams t.matRotation & Translation Matrix:0.999782 -0.000248 0.020861 14.9886000.001702 0.997567 -0.069687 17.641600-0.020793 0.069707 0.997351 29.8813000.000000 0.000000 0.000000 1.000000
Rotation Angles (x,y,z) [rads] = -0.069758 -0.020863 -0.000249
Translations (x,y,z) [mm] = 14.988600 17.641600 29.881300
Scales (x,y,z) = 1.000000 1.000000 1.000000
Skews (xy,xz,yz) = -0.000001 -0.000000 0.000001
Average scaling = 1
Determinant = 0.999999Left-Right orientation: preserved
Forward half transform =0.999945 -0.000306 0.010429 7.4185850.000670 0.999391 -0.034869 9.079558-0.010412 0.034874 0.999338 14.8258610.000000 0.000000 0.000000 1.000000
Backward half transform =0.999946 0.000670 -0.010412 -7.269901-0.000306 0.999392 0.034874 -9.5887990.010429 -0.034869 0.999337 -14.5768100.000000 0.000000 0.000000 1.000000
Maybe I'm missing something someone else sees?
Best,Mike
On Thu, Dec 26, 2013 at 6:46 PM, Pradeep <[log in to unmask]> wrote:
Thanks a lot of the reply Mike!
I tried the avscale command that you suggested and I want to test it by moving the the image 20mm up and realign it to the original.Visually the image matched well but the parameters does not say 20 mm or am I understanding this table totally wrong?
*******@*** 20mm]$ avscale --allparams test.txtRotation & Translation Matrix:0.999782 -0.000249 0.020861 14.9886000.001702 0.997567 -0.069686 17.641600-0.020793 0.069707 0.997351 29.8813000.000000 0.000000 0.000000 1.000000
Rotation Angles (x,y,z) [rads] = -0.069758 -0.020863 -0.000249
Translations (x,y,z) [mm] = 14.988600 17.641600 29.881300
Scales (x,y,z) = 0.822379 0.847364 0.678089
Skews (xy,xz,yz) = -0.001876 0.000530 0.029940
Average scaling = 0.782611
Determinant = 0.472529Left-Right orientation: preserved
Forward half transform =0.906802 -0.001145 0.008802 7.7987850.000607 0.919963 -0.016393 9.311003-0.009442 0.032111 0.823343 16.2459560.000000 0.000000 0.000000 1.000000
Backward half transform =1.102675 0.001730 -0.010535 -8.444473-0.000714 1.086988 0.019132 -10.4262040.013818 -0.046773 1.212749 -19.3745330.000000 0.000000 0.000000 1.000000
Thanks,
Pradeep
On Mon, Dec 23, 2013 at 4:44 PM, Michael Dwyer <[log in to unmask]> wrote:
Hi Pradeep,
Try FSL's very nice avscale utility with the --allparams option. It will print out a decomposition for you. However, take a look at Mark Jenkinson's recent comment on the list (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1311&L=fsl&F=&S=&P=403012) to better understand the caveats of "arbitrary" decomposition. As he mentioned, rmsdiff might be more meaningful.
Best,Mike--
On Mon, Dec 23, 2013 at 6:23 PM, Pradeep <[log in to unmask]> wrote:
Hello All,
We are trying to asses PET scan movement with in the subjects between two frames. I have used FLIRT linear registration to reorient the two images which realigned well. I am currently having troubles to understand the .mat file that was generated.
example *.mat file1.0000 0 0 00 1.0000 0.0011 -0.08090 -0.0011 1.0000 0.11290 0 0 1.0000
It would be great if some one could point me towards a document which will explain linear and rotational parameters in this matrix and if there is a way to report the subject movement in mm or some thing that is easier to understand.
Thanks,Pradeep
Michael G. Dwyer, Ph.D.Assistant Professor of Neurology
Director of Technical Imaging Development
Buffalo Neuroimaging Analysis Center
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Michael G. Dwyer, Ph.D.Assistant Professor of Neurology
Director of Technical Imaging Development
Buffalo Neuroimaging Analysis Center