Protocol for running MBM.py of uCT scans of 15.5 dpc embryos

The following command and associated files will allow for uCT scans of embryos to be analysed via MBM.py: MBM.py --pipeline-name TCP_shrt --mem 100 --num-executors 40
--init-model /home/kyle_arkell/mouse_atlas/image.mnc
--registration-method minctracc --registration-strategy pairwise_and_build_model
--nlin-protocol /home/kyle_arkell/embryo_minctracc_protocol.csv
--no-run-maget --maget-no-mask --no-common-space-registration --verbose --config-file /home/kyle_arkell/arkell.cfg
--lsq12-protocol /home/kyle_arkell/Henrik/TCP-1700003F12Rik/MBM_lsq12_embryo_protocol.csv
--output-dir /home/kyle_arkell/TCP_mrg_v3/ --files /home/kyle_arkell/TCP_short/*mnc

embryo_minctracc_protocol.csv "blur";0.25;0.25;0.25;0.25;0.25;-1 "step";1;0.5;0.5;0.2;0.2;0.1 "iterations";200;200;200;200;200;200 "gradient";False;False;True;False;True;False

MBM_lsq12_embryo_protocol.csv "blur";0.3;0.1 "step";0.3;0.15 "gradient";FALSE;FALSE "simplex";3;1.5 "w_translations";0.4;0.4

arkell_cfg.txt [arkell]

the /mouse_atlas/ directory contains the initial model and segmented mouse atlas available from: http://www.mouseimaging.ca/technologies/mouse_atlas/mouse_embryo_atlas.html

image.mnc = intial model image_mask.mnc = segmented mouse atlas. image_native.mnc = identical copy of the initial model image_native_mask.mnc = identical copy of the segmented mouse atlas

image_native_to_standard.xfm: MNI Transform File %Thu Dec 22 11:56:32 2005>>> manually created identity file %(Package MNI AutoReg, version 0.98k, compiled by baghdadi@thebrain (x86_64-unknown-linux-gnu) on 2005-10-19 at 12:10:06)

Transform_Type = Linear; Linear_Transform = 1 0 0 0 0 1 0 0 0 0 1 0;