Hi Mark,
I trying to rotate a vmr using the dicom-cosines, but without a satisfying
result. I used the basic documentation of dicom from the xmedcon webpage.
During my test I found a procedure from you on this list
(http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind05&L=FSL&D=0&I=-3&X=33245B0F82F857D1DC&Y=magerkurth%40physik.uni-frankfurt.de&P=14763)
Please take look at my procedure, for me both are equal, except the
translation part, but this one should be the smallest problem. Here is my
procedure:
the dicom files are converted with medcon, no rotation is additional applied:
medcon -f <files*> -c anlz -noprefix - stacks -o <out>
the resulting analyze-files are
sag.*: mprage, 88 128 128, 2mm iso resolution, isocentered, sagital
measured, HFS
the needed dicom info is
(0020,0032) DS[3] ImagePositionPatient: [-127] [-88] [128]
(0020,0037) DS[6] ImageOrientationPatient: [0] [1] [0] [0] [0] [-1]
rot.*: equal, but rotated about 10° in sagital and coronal view on the
scanner (siemens trio)
(0020,0032) DS[3] ImagePositionPatient: [-117.13334061765]
[-68.427035244597] [147.83274793964]
(0020,0037) DS[6] ImageOrientationPatient: [0.17624435052857]
[0.98434644760204] [-9.43392231e-009] [-0.1683331589845] [0.03013955000799]
[-0.9852692805074]
from xmedcon:
HFS -> patient system and machine system are equal X=R->L, Y=A->P, Z=F->H
sagital measuring -> row-vec +y, col-vec -z
from http://lcni.uoregon.edu/~jolinda/MRIConvert/fileformats.htm
the column direction is flipped before writing
Using this informations I get the following rotating matrix:
Y x Z cosines Y cosines Z transl
0.9692 0.176 0.168 5
-0.1734 0.984 -0.030 5
-0.1706 0.000 0.985 10
0 0 0 1
Applying this on sag doesn't lead to rot
For finding my mistake, I using Nudge for rotation sag. The use angles are
X=-10°, Y=-10°, Z=0°
The received matrix looks confusing, because it's more than an exchange of
col-vectors between the two matrices:
0.984747 0.029615 0.171453 -24.2087
0.000000 0.985408 -0.170209 23.4698
-0.173992 0.167613 0.970378 -2.38755
0 0 0 1
Where is the mistake?
This the my second post, the first was rejected, caused by a 1MB attachment.
If you need the used files, contact me.
Best regards,
Joerg
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