Installation

It should be relatively easy to build the beta version of the MNI_ANIMAL package. The tarfile mni_animal-x.yy.tar.gz must be untarred within the root of the mni_autoreg directory tree after the MNI_AutoReg package has been built.

I assume that all MNI_AutoReg targets are built and installed before building animal. Note that a make clean should not be done, since some of the programs are needed to run the tests below.

1.

Get, build, test and install the MNI_Autoreg package. See the MNI_AutoReg home page (you'll need mni_autoreg-0.98d or later).

Do not run make clean - MNI_ANIMAL needs all the files in the MNI_Autoreg directory.

2.

Untar the the MNI_ANIMAL package mni_animal-x.yy.tar.gz from within the root of the MNI_AutoReg package.

cd /your/dir/package/mni_autoreg-0.98

guntar -xvfz mni_animal-0.5.tar.gz

3.

Once untarred, there should be a file called build_animal in the MNI_AutoReg directory. Look at it to make sure that things look ok, and then execute it. The build_animal script will overwrite a few source files in the minctracc subdirectory and then rebuild the nonlinear version of minctracc and rename it to animal. It will also build the mincbbox program.

Once compilation is completed, the build_animal script will run a simple test on minctracc/animal to exercise the code. When completed, the volume correlation should close to 0.00465932. If you are interested, you can use mincresample to transform Testing/object1.mnc like Testing/object2.mnc using the recovered transformation and then look at the result with register. For example type:

cd /your/dir/package/mni_autoreg-0.98/Testing

mincresample object1.mnc object1_rsl.mnc -like object2.mnc -transformation ../animal.xfm

register object1_rsl.mnc object2.mnc

4.

nlfit is a development version of the non-linear stereotaxic registration script that will eventually replace mritotal (from the MNI_AutoReg package). It calls animal to do the non-linear registrations in a heirarchical multi-resolution strategy, and permits the user to control the start and stop resolutions of the fit.

There are three lines that may have to be changed so that nlfit will be able to locate configuration and model files normally used with mritotal. You should use your installed version of mritotal to get the values for your system. The following lines of nlfit have to be edited by hand:

line 1:

verify the path to perl5

line 572:

$ModelDir = "/data/avgbrain1/brain/images/model"; make sure that the $ModelDir is the same as line 500 of mritotal

line 612:

@ConfigPath = ($ENV"HOME", "/usr/local/mni/etc/mni_autoreg"); make sure that the path is the same as line 530 of mritotal

5.

Once completed, you will have to manually install the following files to your bin directory:

• minctracc/animal
• minctracc/reversedef
• mincbbox/mincbbox
• ./nlfit
• ./xfmtool
• ./make_model

and copy the following file to your model directory (the same as line 572 of nlfit-0.5):

• ./average_305_headmask.mnc

Check out the NONLIN_README file for more specific information (man page-like) on ANIMAL.