Hi,
I'm trying out your LPC registration to perform registration between epis and the freesurfer anatomicals. In the AFNI viewer, it looks basically right. Now I'd like to take the results and use them in FreeSurfer, but I'm not sure how to do this. Here's what I've done (AFNI version: 2008_07_18_1710, align_epi_anat.py version: 1.17).
I first convert orig.mgz to nifti with mri_convert, then to BRIK with 3dcopy to create anat+orig.BRIK.
I then convert our epi from nifti to epi+orig.BRIK using 3dcopy.
Then I run:
align_epi_anat.py -anat anat+orig -epi epi+orig -epi_base 0 -epi2anat -AddEdge -giant_move
I then view epi_al+orig as an overlay to anat+orig, and, except for cropping, it looks ok.
The matrix from epi_al_mat.aff12.1D is:
1.0009 -0.0017 0.0005 6.4680
-0.0026 0.9929 -0.2306 26.9704
-0.0045 0.2483 0.9705 82.4093
Can you tell me how to interpret this matrix? How do you construct your matrix to map from voxel indices (col, row, slice) to real-world space (x, y, z, in mm)?
Thanks,
doug