Configuration and Protocol Files

nlfit uses the same two external configuration files as mritotal, and are installed when MNI_AutoReg is installed. There is nothing extra to install for MNI_ANIMAL.

The two files are the configuration file (mritotal.cfg) and protocol file (default is mritotal.default.cfg, but you can specify others using the -protocol option). If you follow all the instructions for installation of MNI_AutoReg, then these files will be correctly customized and installed for your site. If things go wrong, though, you should know the following:

• The directory where the configuration and protocol file(s) are installed defaults to /usr/local/etc/mni_autoreg. If you change this (ie. move the files after installing them) without changing Makefile.include and doing "make build" in the "perl/" subdirectory, then mritotal will not be able to find them. That's because "make build" modifies mritotal so that it points to the directory for config files.
• The location of the model files is specified in the configuration file. You should check that the directory where you installed the model files (which is specified in the Makefile for the mni_autoreg_model package) is the same as the directory given in mritotal.cfg (using the -modeldir option). For instance, if mni_autoreg_model/Makefile has the line:

  MODELDIR = /data/avgbrain1/brain/images/model

  then mni_autoreg-0.98/perl/mritotal.cfg should have the line:

  -modeldir /data/avgbrain1/brain/images/model

  and, if you want to be really complete, mni_autoreg-0.98/Makefile.include should have the line

  MODELDIR = /data/avgbrain1/brain/images/model

• If you find it necessary to make a new protocol for your site's data (for instance, if your MRI data consistently covers considerably more than the brain, but the heuristic used by the default protocol doesn't work - see the mritotal man page for more information), then you should copy and change the default protocol file. For instance, you might want to call the protocol "mysite" - in that case, copy mritotal.default.cfg to mritotal.mysite.cfg, and be sure to edit mritotal.cfg so that it uses the new protocol by default. That is, make sure it has "-protocol mysite" instead of "-protocol default".

That said, please notify Louis Collins <louis@bic.mni.mcgill.ca> if the heuristics used by the default protocol don't work for your data.