The NYU Center for Brain Imaging http://cbi.nyu.edu has developed a set of matlab tools for reconstructing fMRI images. The CBI WebDB server automatically reconstructs images. However, you may want to run the reconstruction locally. Here are some quick notes on how to get the recon code running on your machine.
Get the software
Use the heegerlab version
Just add the path to the cbiRecon directory.
ยป addpath(genpath('/share/wotan/heegerlab/cbiRecon'))
This version may not be up-to-date though (it depends on whether I have updated it). If you want to have control over updating of the repository follow the directions in the next several steps.
download the recon code from CBI
setenv CVSROOT :ext:eli@cbi.nyu.edu:/cvsroot setenv CVS_RSH ssh cvs checkout -P src/CBIRecon cvs checkout -P src/NIfTImatlab mv src cbiSrc
download the NIfTI C library from SourceForge
cvs -d:pserver:anonymous@niftilib.cvs.sourceforge.net:/cvsroot/niftilib login # No password is necessary. Hit enter when prompted for a password cvs -z3 -d:pserver:anonymous@niftilib.cvs.sourceforge.net:/cvsroot/niftilib co -P Clibs mv Clibs niftiClibs
This library is needed to compile Valerio's nifti code. But, I (justin) couldn't get it to compile on my computer (a PPC Mac). It gave the following error:
echo "arch is " arch is (cd znzlib; make depend; make lib;) Makefile:33: depend.mk: No such file or directory gcc -MM -I/usr/include znzlib.c >> depend.mk csh: depend.mk: No such file or directory. make[[1]]: *** [[depend.mk]] Error 1 Makefile:33: depend.mk: No such file or directory gcc -MM -I/usr/include znzlib.c >> depend.mk csh: depend.mk: No such file or directory. make[[1]]: *** [[depend.mk]] Error 1 make: *** [[znz]] Error 2
I never figured out the problem, but instead of recompiling all of this, consider using the library in the heegerlab partition:
/share/wotan/heegerlab/cbiRecon/@niftiheader /share/wotan/heegerlab/cbiRecon/@niftifile
Build the NIfTI stuff
building NIfTI Clibs
cd niftiClibs make
build CBI's NIfTImatlab
(note: this is complicated b/c the autoconf stuff is screwed up
cd cbiSrc/NIfTImatlab autoconf ./configure
expect some warnings like:
config.status: creating Makefile config.status: WARNING: Makefile.in seems to ignore the --datarootdir setting
now edit the file called: src/Makefile.in
change LOCAL_LIBS to add the path to your niftiClibs lib directory. For me, that is:
LOCAL_LIBS = -L${libdir} -L/users2/eli/src/niftiClibs/lib/ -lniftiio -lznz -lz
do the same for CFLAGS:
CFLAGS = -D$(OS) -I@srcdir@ -I$(loc_incdir) -I$(includedir) -I$(includedir)/nifti $(GCINCLUDEFLAG) -I/users2/eli/src/niftiClibs/include/ -DHAVE_ZLIB
now reconfigure:
./configure
and make:
make
All should build okay
Add the NIfTI and recon code directories to your matlab path
for my setup, my ~/matlab/startup.m file looks like:
addpath(genpath('/Local/Users/eli/proj/cbiSrc/NIfTImatlab/matlab'));
addpath(genpath('/Local/Users/eli/proj/cbiSrc/CBIRecon/matlab'));
run the recon code
recon_seg('061212110942.raw', 'test2', 2)