Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Comment: added a missing --files and other options (though they are guesses) to the MAGeT example

...

Code Block
languagebash
MAGeT.py \
--atlas-library=/hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_Qiu_2016_Egan_2015_40micron/ex-vivo \
--pipeline-name=full_MAGeT \
--max-templates=5 \
--num-executors=30 [general rule of thumb is to use as many as the number of subjects in your pipeline]\
--lsq12-protocol=/hpf/largeprojects/MICe/tools/protocols/linear/default_linear_MAGeT_prot.csv  \
--nlin-protocol=/hpf/largeprojects/MICe/tools/protocols/nonlinear/default_nlin_MAGeT_minctracc_prot.csv \
--registration-method=minctracc \
--no-mask
--files [*lsq6 resampled files from MBM pipeline*].mnc

...