Add an atlas_to_atlas and a mouse_to_mouse script to the repository

[mcvaneede]

The atlas_to_atlas perl script could be used for this, but it might be nice to convert it to a Python script and add the following options:

1. optional lsq6
2. make lsq12 optional as well, but perform by default
3. options to add masks (potentially different for the source and target)
4. resample the source file to lsq12 (or 9) and nlin1 for debug purposes

Here are some mouse brain parameters I used, which worked very well in a mouse brain to mouse brain scenario:

my $minctracc_opts = "-xcorr -clobber -debug -w_translations 0.4 0.4 0.4 -tol 0.0001 ";
if(defined($mask)){
$minctracc_opts .= " -model_mask ${mask} -source_mask ${mask} ";
}

Spawn("minctracc $minctracc_opts -step 1 1 1 -lsq6 -simplex 3 -identity ${outputdir}${source_base}_0.336_blur.mnc ${outputdir}${target_base}_0.336_blur.mnc ${outputdir}${lsq6_1_xfm}");
Spawn("minctracc $minctracc_opts -step 1 1 1 -lsq6 -simplex 3 -transform ${outputdir}${lsq6_1_xfm} ${outputdir}${source_base}_0.336_dxyz.mnc ${outputdir}${target_base}_0.336_dxyz.mnc ${outputdir}${lsq6_2_xfm}");
Spawn("minctracc $minctracc_opts -step 0.5 0.5 0.5 -lsq6 -simplex 1.5 -transform ${outputdir}${lsq6_2_xfm} ${outputdir}${source_base}_0.224_blur.mnc ${outputdir}${target_base}_0.224_blur.mnc ${outputdir}${lsq6_3_xfm}");
Spawn("minctracc $minctracc_opts -step 0.336 0.336 0.336 -lsq6 -simplex 1.008 -transform ${outputdir}${lsq6_3_xfm} ${outputdir}${source_base}_0.112_blur.mnc ${outputdir}${target_base}_0.112_blur.mnc ${outputdir}${lsq6_4_xfm}");

Spawn("minctracc $minctracc_opts -step 1 1 1 -lsq9 -simplex 3 -transform ${outputdir}${lsq6_4_xfm} ${outputdir}${source_base}_0.336_blur.mnc ${outputdir}${target_base}_0.336_blur.mnc ${outputdir}${lsq12_1_xfm}");
Spawn("minctracc $minctracc_opts -step 1 1 1 -lsq9 -simplex 3 -transform ${outputdir}${lsq12_1_xfm} ${outputdir}${source_base}_0.336_dxyz.mnc ${outputdir}${target_base}_0.336_dxyz.mnc ${outputdir}${lsq12_2_xfm}");
Spawn("minctracc $minctracc_opts -step 0.5 0.5 0.5 -lsq9 -simplex 1.5 -transform ${outputdir}${lsq12_2_xfm} ${outputdir}${source_base}_0.224_blur.mnc ${outputdir}${target_base}_0.224_blur.mnc ${outputdir}${lsq12_3_xfm}");
Spawn("minctracc $minctracc_opts -step 0.336 0.336 0.336 -lsq9 -simplex 1.008 -transform ${outputdir}${lsq12_3_xfm} ${outputdir}${source_base}_0.112_blur.mnc ${outputdir}${target_base}_0.112_blur.mnc ${outputdir}${lsq12_4_xfm}");
Spawn("minctracc $minctracc_opts -step 0.16 0.16 0.16 -lsq9 -simplex 0.48 -transform ${outputdir}${lsq12_4_xfm} $source_atlas $target_atlas ${outputdir}${lsq12_5_xfm}");