Hello all you AFNI experts
I need to work on some images that are oblique coronals. I have been given the co-ordinates for the centers of the first and last slice of the volume. So I have P 35.1, A 35.5, I 11.7 and S 2.4, R and L being 0.0. I also know the angle which is 169 degrees ( the superior part of the coronal slices are tilted more anterior than the rest of the slice) . There have been 25 slices which are 3 mm thick. How do I reconstruct the images?
The command line that I used was
to3d -anat -prefix Proton_Density_TE2 -session Results -2swap -view orig -xFOV 120L-120R -yFOV 117.6S-131.7I -zSLAB 35.1P-35.5A '3D:0:8432:256:256:1:Proton-Density_TE2/I*'
But this is incorrect as 35.1+35.5 =70.6 and not 75 (which is 25*3). besides the values for S and I too are not correct as I just added and subtracted from 120. The images that I got out of this are perfect T2 weighted images but they are wrong considering that the volume either has been squeezed or stretched to account for the errors I made. I am now thinking 3drotate, the nudge plugin but I dont really know. Please do help me out.
Thanks
NL