mritotal requires two external files to run. These 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 above instructions, then these files will be correctly customized and installed for your site. If things go wrong, though, you should know the following:
/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.
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
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
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.