From Jason Lerch, 20 Feb. 2003

1) Used register to calculate angle of rotation from long. axis of HC
   to horizontal (computed on icbm_avg_152_t1_lin.mnc).

2) Used param2xfm to generate a new transform file (rotate it about
   the x-axis:

param2xfm -rotations 38.6 0 0 output.xfm

3) resampled template file s.t. y-axis is parallel to long. axis of HC

mincresample
/data/sendai/sendai1/quarantine/model_data/mni_autoreg/icbm_avg_152_t1_tal_lin.mnc
-use_input_sampling -transform rotate_y.xfm icbm_152_rotated_t1_lin.mnc

4) use mritoself to generate new transforms for each subject file

mritoself -transform rotate_y.xfm subject_t1_final.mnc -target
icbm_152_rotated_t1_lin.mnc subject_rotated_t1.xfm

5) use mincresample on each subject's mri file to rotate it about the
   x-axis:

mincresample -transformation subject_rotated_t1.xfm -like
icbm_152_rotated_t1_lin.mnc subject_t1_final.mnc
subject_t1_final_rotated.mnc 

6) Similarly, use mincresample to rotate the label files for each
   subject:

mincresample -transformation subject_rotated_t1.xfm -like
icbm_152_rotated_t1_lin.mnc sub_label_file.mnc sub_labels_rotated.mnc