manual recons

[rfdougherty]

I'm trying to run some manual mux recons using the new nimsdata. It seems that you guys took away my main in nimsraw (now nimspfile). OK, so I need to use nimsdata. Fine. But how do I pass the recon args to nimsdata? I see the '--parser_kwarg' arg, but I can't figure out how to use it. I tried a few things, but all produced some error or another. Can you add a few examples to the help text for nimsdata? It should also be possible for nimsdata to list all the possible options for each of its submodules.

[kevlarkevin]

--parser_kwarg recon_type=sense. Use --parser_kwarg multiple times to add multiple keyword arguments.

nimsdata.py -p pfile \ 
    path/to/pfile
    --parser_kwarg recon_type=sense \
    --parser_kwarg aux_file=/some/other/pfile.tgz \
    -w nifti \
    outputprefix

a few things to note:

• --parser_kwarg load_data=True is always implied.
• the aux file given to--parser_kwarg aux_file=/some/other/pfile.tgz currently has to be a tgz.