Preprocess Rat Brains Structural In vivo

For our in vivo rats scanned with the Surface coil 2 x 2 in the Bruker 7T FLASH 3D sequence (160 um) 11 min.

Extract using Bruker2Nifti software.

We usually do 2 repetitions, so each NIFTI will have 2 runs (4D). Split it with fslsplit flag -t, then co-register

module load sge/2011.11p1 python36/3.6.8 imagemagick/7.0.5.4 minc-toolkit-v2/1.9.17 torch7/29jul2019 minc2-simple/2.2.30 minc-toolkit-extras/24abr2019 hdf5/1.8.18 netcdf/gcc/64/4.3.3.1 gcc/5.2.0 pydpiper/2.0.13 parallel/20190522 qbatch/2.1.3

module load minc-stuffs/0.1.24 ants/9may2019