From minc-users@bic.mni.mcgill.ca Wed Dec 3 20:05:33 2003 From: minc-users@bic.mni.mcgill.ca (Simon DROUIN) Date: Wed, 3 Dec 2003 15:05:33 -0500 Subject: [MINC-users] mivarget (beginner's question) Message-ID: Hi All, Does someone know if what we get in data after calling the following line of code is affected in any way by the direction cosines in the file: mivarget( minc_file_id, image_var_id, start, sizes, NC_BYTE, MI_UNSIGNED, (void*) data ) where data is a pointer to an unsigned char where minc_file_id is the id of the opened minc file. where image_var_id is the id of the image variable. knowing the variable data type for image is unsigned char. If so, How do I get raw pixel values from a minc file (without using volume_io)? Thanks in advance. Simon Drouin From minc-users@bic.mni.mcgill.ca Wed Dec 3 20:17:52 2003 From: minc-users@bic.mni.mcgill.ca (Robert VINCENT) Date: Wed, 3 Dec 2003 15:17:52 -0500 Subject: [MINC-users] mivarget (beginner's question) In-Reply-To: Message-ID: Simon, As far as I am aware, mivarget() will not use the direction cosines in any way. The start[] array is specified in voxel coordinates. The function will perform only rudimentary data type conversions on the data, it does not do any voxel/real scaling. If you need to do any complex transformations on the data, you want to use miicv_get() or volume_io. -bert On Wed, 3 Dec 2003, Simon DROUIN wrote: > Hi All, > > Does someone know if what we get in data after calling the following line > of code is affected in any way by the direction cosines in the file: > > mivarget( minc_file_id, image_var_id, start, sizes, NC_BYTE, MI_UNSIGNED, (void*) data ) > > where data is a pointer to an unsigned char > where minc_file_id is the id of the opened minc file. > where image_var_id is the id of the image variable. > knowing the variable data type for image is unsigned char. > > If so, How do I get raw pixel values from a minc file (without using > volume_io)? > > Thanks in advance. > > Simon Drouin > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From minc-users@bic.mni.mcgill.ca Wed Dec 10 07:11:55 2003 From: minc-users@bic.mni.mcgill.ca (siamak Ardekani) Date: 09 Dec 2003 23:11:55 -0800 Subject: [MINC-users] installation problem with N3 on Linux (red hat 9) Message-ID: <1071040315.22612.13.camel@localhost> Dear All, I was checking the archive and noticed a message posted by one of the members describing a problem similar to mine. Basically, I am trying to install MNI_N3 version 1.07 on a Linux box running red hat 9. I got the following error while executing the configure: [root@localhost N3]# ./configure --prefix=/usr/local/MNI checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for style of include used by make... GNU checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking dependency style of gcc... gcc3 checking whether gcc and cc understand -c and -o together... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking for ranlib... ranlib checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for library m... yes checking for g77... g77 checking whether we are using the GNU Fortran 77 compiler... yes checking whether g77 accepts -g... yes checking how to get verbose linking output from g77... -v checking for Fortran libraries of g77... -L/usr/lib/gcc-lib/i386-redhat-linux/3.2.2 -L/usr/lib/gcc-lib/i386-redhat-linux/3.2.2/../../.. -lfrtbegin -lg2c -lm -lgcc_s checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, extra underscore checking for sgemm_... no checking for ATL_xerbla in -latlas... no checking for sgemm_ in -framework vecLib... no checking for sgemm_ in -lblas... no checking for sgemm_ in -lcxml... no checking for sgemm_ in -ldxml... no checking for sgemm_ in -lscs... no checking for sgemm_ in -lcomplib.sgimath... no checking for sgemm_ in -lblas... (cached) no checking for sgemm_ in -lblas... (cached) no checking for library F77... no configure: error: cannot find required library F77 I have already installed CLAPACK in /usr/local directory. Although, I am not sure if configure can recognize the library. I appreciate comments in this regard. Thanks, Siamak From minc-users@bic.mni.mcgill.ca Wed Dec 10 17:32:24 2003 From: minc-users@bic.mni.mcgill.ca (Steve ROBBINS) Date: Wed, 10 Dec 2003 12:32:24 -0500 Subject: [MINC-users] installation problem with N3 on Linux (red hat 9) In-Reply-To: <1071040315.22612.13.camel@localhost>; from ardekani@seas.ucla.edu on Tue, Dec 09, 2003 at 11:11:55PM -0800 References: <1071040315.22612.13.camel@localhost> Message-ID: <20031210123224.D390347@shadow.bic.mni.mcgill.ca> On Tue, Dec 09, 2003 at 11:11:55PM -0800, siamak Ardekani wrote: > Dear All, > > I was checking the archive and noticed a message posted by one of the > members describing a problem similar to mine. Basically, I am trying to > install MNI_N3 version 1.07 on a Linux box running red hat 9. I got the > following error while executing the configure: > > [root@localhost N3]# ./configure --prefix=/usr/local/MNI [...] > checking for library F77... no > configure: error: cannot find required library F77 > > I have already installed CLAPACK in /usr/local directory. Although, I am > not sure if configure can recognize the library. To diagnose this problem, you need to look through "config.log" for the error messages. With regards to blas/lapack, you have two options. #1 Install vendor packages. You need to have the "developer" package installed. For Debian, the package names are "blas-dev" and "lapack-dev". I'm guessing that redhat has something similar. #2 Install clapack as described in N3's INSTALL file. In particular, N3 requires the the three libraries be named "libF77.a", "libblas.a", and "liblapack.a" and that their associated header files ("f2c.h" and "blaswrap.h") be installed on the system. You need to manually copy the libraries and header files to the appropriate pathnames on your system. The three ".a" files should be in /usr/local/lib, and the ".h" files should be in /usr/local/include. Regards, -Steve From minc-users@bic.mni.mcgill.ca Thu Dec 11 05:08:07 2003 From: minc-users@bic.mni.mcgill.ca (siamak Ardekani) Date: 10 Dec 2003 21:08:07 -0800 Subject: [MINC-users] installation problem with N3 on Linux (red hat 9) In-Reply-To: <20031210123224.D390347@shadow.bic.mni.mcgill.ca> References: <1071040315.22612.13.camel@localhost> <20031210123224.D390347@shadow.bic.mni.mcgill.ca> Message-ID: <1071119286.22995.21.camel@localhost> Dear Steve, Thank you for the reply. I installed blas/lapack and now the configuration recognize the library. However, now it complains about netcdf library. I used the rpm file provided at http://www.bic.mni.mcgill.ca/software/distribution to install the netcdf and MINC. [root@localhost MNI_N3]# rpm -qpl netcdf-3.5.0-linux-2.4-intel.rpm /usr/local/mni/bin /usr/local/mni/bin/ncdump /usr/local/mni/bin/ncgen /usr/local/mni/include /usr/local/mni/include/netcdf.h /usr/local/mni/lib /usr/local/mni/lib/libnetcdf.a /usr/local/mni/man /usr/local/mni/man/man1 /usr/local/mni/man/man1/ncdump.1 /usr/local/mni/man/man1/ncgen.1 /usr/local/mni/man/man3 /usr/local/mni/man/man3/netcdf.3 when I launch configure: [root@localhost N3]# ./configure --prefix=/usr/local/mni checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes [....] checking for sgemm_ in -lblas... (cached) yes checking for sgemm_ in -lessl... no checking for sgemm_ in -lblas... (cached) yes checking for cheev_... no checking for cheev_ in -llapack... yes checking for library EBTKS... yes checking for library m... yes checking for library netcdf... no configure: error: cannot find required library netcdf [root@localhost N3]# looking at config.log : configure:6803: /usr/bin/cc -o conftest -O -Df2cFortran -DNDEBUG conftest.c -lm -lEBTKS -lm >&5 configure:6809: $? = 0 configure:6812: test -z || test ! -s conftest.err configure:6815: $? = 0 configure:6818: test -s conftest configure:6821: $? = 0 configure:6832: result: yes configure:6841: checking for library netcdf configure:6868: /usr/bin/cc -o conftest -O -Df2cFortran -DNDEBUG conftest.c -ln etcdf -lm -lEBTKS -lm >&5 conftest.c:16:20: netcdf.h: No such file or directory configure:6874: $? = 1 configure: failed program was: | /* confdefs.h. */ | | #define PACKAGE_NAME "" | #define PACKAGE_TARNAME "" | #define PACKAGE_VERSION "" | #define PACKAGE_STRING "" | #define PACKAGE_BUGREPORT "" | #define PACKAGE "N3" | #define VERSION "1.07" | #ifdef __cplusplus | extern "C" void std::exit (int) throw (); using std::exit; | #endif | #define HAVE_BLAS 1 | #define HAVE_LAPACK 1 | /* end confdefs.h. */ | #include | #ifdef F77_DUMMY_MAIN | | # ifdef __cplusplus | extern "C" | # endif | int F77_DUMMY_MAIN() { return 1; } | | #endif | int | main () | { | int i = ncopen("",0); | ; | return 0; | } configure:6897: result: no configure:6900: error: cannot find required library netcdf I was wondering why it complains about netcdf.h where it is already installed in the correct location? Thanks, Siamak On Wed, 2003-12-10 at 09:32, Steve ROBBINS wrote: > On Tue, Dec 09, 2003 at 11:11:55PM -0800, siamak Ardekani wrote: > > Dear All, > > > > I was checking the archive and noticed a message posted by one of the > > members describing a problem similar to mine. Basically, I am trying to > > install MNI_N3 version 1.07 on a Linux box running red hat 9. I got the > > following error while executing the configure: > > > > [root@localhost N3]# ./configure --prefix=/usr/local/MNI > > [...] > > > checking for library F77... no > > configure: error: cannot find required library F77 > > > > I have already installed CLAPACK in /usr/local directory. Although, I am > > not sure if configure can recognize the library. > > To diagnose this problem, you need to look through "config.log" for > the error messages. > > With regards to blas/lapack, you have two options. > > #1 Install vendor packages. You need to have the "developer" package > installed. For Debian, the package names are "blas-dev" and "lapack-dev". > I'm guessing that redhat has something similar. > > > #2 Install clapack as described in N3's INSTALL file. In particular, > > N3 requires the the three libraries be named "libF77.a", > "libblas.a", and "liblapack.a" and that their associated header files > ("f2c.h" and "blaswrap.h") be installed on the system. You need to > manually copy the libraries and header files to the appropriate > pathnames on your system. > > The three ".a" files should be in /usr/local/lib, and the ".h" files > should be in /usr/local/include. > > Regards, > -Steve > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From minc-users@bic.mni.mcgill.ca Thu Dec 11 14:29:16 2003 From: minc-users@bic.mni.mcgill.ca (Steve ROBBINS) Date: Thu, 11 Dec 2003 09:29:16 -0500 Subject: [MINC-users] installation problem with N3 on Linux (red hat 9) In-Reply-To: <1071119286.22995.21.camel@localhost>; from ardekani@seas.ucla.edu on Wed, Dec 10, 2003 at 09:08:07PM -0800 References: <1071040315.22612.13.camel@localhost> <20031210123224.D390347@shadow.bic.mni.mcgill.ca> <1071119286.22995.21.camel@localhost> Message-ID: <20031211092916.F390347@shadow.bic.mni.mcgill.ca> On Wed, Dec 10, 2003 at 09:08:07PM -0800, siamak Ardekani wrote: > Dear Steve, > > Thank you for the reply. I installed blas/lapack and now the > configuration recognize the library. However, now it complains about > netcdf library. I used the rpm file provided at > http://www.bic.mni.mcgill.ca/software/distribution to install the netcdf > and MINC. > > > [root@localhost MNI_N3]# rpm -qpl netcdf-3.5.0-linux-2.4-intel.rpm > /usr/local/mni/bin > /usr/local/mni/bin/ncdump > /usr/local/mni/bin/ncgen > /usr/local/mni/include > /usr/local/mni/include/netcdf.h ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ That's in /usr/local/mni/include, a path not normally searched by the C compiler. You need to tell the compiler to look there. Re-run configure as follows ./configure --with-build-path=/usr/local/mni --prefix=/usr/local/mni Cheers, -Steve > /usr/local/mni/lib > /usr/local/mni/lib/libnetcdf.a > /usr/local/mni/man > /usr/local/mni/man/man1 > /usr/local/mni/man/man1/ncdump.1 > /usr/local/mni/man/man1/ncgen.1 > /usr/local/mni/man/man3 > /usr/local/mni/man/man3/netcdf.3 > > > when I launch configure: > > > [root@localhost N3]# ./configure --prefix=/usr/local/mni > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > checking for gawk... gawk > checking whether make sets $(MAKE)... yes > > [....] > > > > checking for sgemm_ in -lblas... (cached) yes > checking for sgemm_ in -lessl... no > checking for sgemm_ in -lblas... (cached) yes > checking for cheev_... no > checking for cheev_ in -llapack... yes > checking for library EBTKS... yes > checking for library m... yes > checking for library netcdf... no > configure: error: cannot find required library netcdf > [root@localhost N3]# > > > looking at config.log : > > > > configure:6803: /usr/bin/cc -o conftest -O -Df2cFortran -DNDEBUG > conftest.c -lm > -lEBTKS -lm >&5 > configure:6809: $? = 0 > configure:6812: test -z || test ! -s > conftest.err > configure:6815: $? = 0 > configure:6818: test -s conftest > configure:6821: $? = 0 > configure:6832: result: yes > configure:6841: checking for library netcdf > configure:6868: /usr/bin/cc -o conftest -O -Df2cFortran -DNDEBUG > conftest.c -ln > etcdf -lm -lEBTKS -lm >&5 > conftest.c:16:20: netcdf.h: No such file or directory > configure:6874: $? = 1 > configure: failed program was: > | /* confdefs.h. */ > | > | #define PACKAGE_NAME "" > | #define PACKAGE_TARNAME "" > | #define PACKAGE_VERSION "" > | #define PACKAGE_STRING "" > | #define PACKAGE_BUGREPORT "" > | #define PACKAGE "N3" > | #define VERSION "1.07" > | #ifdef __cplusplus > | extern "C" void std::exit (int) throw (); using std::exit; > | #endif > | #define HAVE_BLAS 1 > | #define HAVE_LAPACK 1 > | /* end confdefs.h. */ > | #include > | #ifdef F77_DUMMY_MAIN > | > | # ifdef __cplusplus > | extern "C" > | # endif > | int F77_DUMMY_MAIN() { return 1; } > | > | #endif > | int > | main () > | { > | int i = ncopen("",0); > | ; > | return 0; > | } > configure:6897: result: no > configure:6900: error: cannot find required library netcdf > > > > I was wondering why it complains about netcdf.h where it is already > installed in the correct location? > > Thanks, > > Siamak > > > > > On Wed, 2003-12-10 at 09:32, Steve ROBBINS wrote: > > On Tue, Dec 09, 2003 at 11:11:55PM -0800, siamak Ardekani wrote: > > > Dear All, > > > > > > I was checking the archive and noticed a message posted by one of the > > > members describing a problem similar to mine. Basically, I am trying to > > > install MNI_N3 version 1.07 on a Linux box running red hat 9. I got the > > > following error while executing the configure: > > > > > > [root@localhost N3]# ./configure --prefix=/usr/local/MNI > > > > [...] > > > > > checking for library F77... no > > > configure: error: cannot find required library F77 > > > > > > I have already installed CLAPACK in /usr/local directory. Although, I am > > > not sure if configure can recognize the library. > > > > To diagnose this problem, you need to look through "config.log" for > > the error messages. > > > > With regards to blas/lapack, you have two options. > > > > #1 Install vendor packages. You need to have the "developer" package > > installed. For Debian, the package names are "blas-dev" and "lapack-dev". > > I'm guessing that redhat has something similar. > > > > > > #2 Install clapack as described in N3's INSTALL file. In particular, > > > > N3 requires the the three libraries be named "libF77.a", > > "libblas.a", and "liblapack.a" and that their associated header files > > ("f2c.h" and "blaswrap.h") be installed on the system. You need to > > manually copy the libraries and header files to the appropriate > > pathnames on your system. > > > > The three ".a" files should be in /usr/local/lib, and the ".h" files > > should be in /usr/local/include. > > > > Regards, > > -Steve > > > > > > _______________________________________________ > > MINC-users@bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From minc-users@bic.mni.mcgill.ca Fri Dec 12 08:19:24 2003 From: minc-users@bic.mni.mcgill.ca (siamak ardekani) Date: Fri, 12 Dec 2003 00:19:24 -0800 Subject: [MINC-users] installation problem with N3 on Linux (red hat 9) References: <1071040315.22612.13.camel@localhost> <20031210123224.D390347@shadow.bic.mni.mcgill.ca> <1071119286.22995.21.camel@localhost> <20031211092916.F390347@shadow.bic.mni.mcgill.ca> Message-ID: <002c01c3c088$ad03d2a0$2f6363c0@itmedicine.net> Dear Steve, Thanks again for the comment. Finally, I was able install N3 and make it run. To test the performance I tried to run nu_correct on one of the data files located in the N3/testing folder named block.mnc. However, I didn't see any difference before and after correction. I also ran the program on a real MRI brain data without any success (using different combinations of -stop, -distance, -iteration and -fwhm). Is there any appropriate way to check the algorithm and make sure that installation has been done ok. Thanks, Siamak ----- Original Message ----- From: "Steve ROBBINS" To: Sent: Thursday, December 11, 2003 6:29 AM Subject: Re: [MINC-users] installation problem with N3 on Linux (red hat 9) > On Wed, Dec 10, 2003 at 09:08:07PM -0800, siamak Ardekani wrote: > > Dear Steve, > > > > Thank you for the reply. I installed blas/lapack and now the > > configuration recognize the library. However, now it complains about > > netcdf library. I used the rpm file provided at > > http://www.bic.mni.mcgill.ca/software/distribution to install the netcdf > > and MINC. > > > > > > [root@localhost MNI_N3]# rpm -qpl netcdf-3.5.0-linux-2.4-intel.rpm > > /usr/local/mni/bin > > /usr/local/mni/bin/ncdump > > /usr/local/mni/bin/ncgen > > /usr/local/mni/include > > /usr/local/mni/include/netcdf.h > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > > That's in /usr/local/mni/include, a path not normally searched by > the C compiler. You need to tell the compiler to look there. > > Re-run configure as follows > > ./configure --with-build-path=/usr/local/mni --prefix=/usr/local/mni > > Cheers, > -Steve > > > > > > > /usr/local/mni/lib > > /usr/local/mni/lib/libnetcdf.a > > /usr/local/mni/man > > /usr/local/mni/man/man1 > > /usr/local/mni/man/man1/ncdump.1 > > /usr/local/mni/man/man1/ncgen.1 > > /usr/local/mni/man/man3 > > /usr/local/mni/man/man3/netcdf.3 > > > > > > when I launch configure: > > > > > > [root@localhost N3]# ./configure --prefix=/usr/local/mni > > checking for a BSD-compatible install... /usr/bin/install -c > > checking whether build environment is sane... yes > > checking for gawk... gawk > > checking whether make sets $(MAKE)... yes > > > > [....] > > > > > > > > checking for sgemm_ in -lblas... (cached) yes > > checking for sgemm_ in -lessl... no > > checking for sgemm_ in -lblas... (cached) yes > > checking for cheev_... no > > checking for cheev_ in -llapack... yes > > checking for library EBTKS... yes > > checking for library m... yes > > checking for library netcdf... no > > configure: error: cannot find required library netcdf > > [root@localhost N3]# > > > > > > looking at config.log : > > > > > > > > configure:6803: /usr/bin/cc -o conftest -O -Df2cFortran -DNDEBUG > > conftest.c -lm > > -lEBTKS -lm >&5 > > configure:6809: $? = 0 > > configure:6812: test -z || test ! -s > > conftest.err > > configure:6815: $? = 0 > > configure:6818: test -s conftest > > configure:6821: $? = 0 > > configure:6832: result: yes > > configure:6841: checking for library netcdf > > configure:6868: /usr/bin/cc -o conftest -O -Df2cFortran -DNDEBUG > > conftest.c -ln > > etcdf -lm -lEBTKS -lm >&5 > > conftest.c:16:20: netcdf.h: No such file or directory > > configure:6874: $? = 1 > > configure: failed program was: > > | /* confdefs.h. */ > > | > > | #define PACKAGE_NAME "" > > | #define PACKAGE_TARNAME "" > > | #define PACKAGE_VERSION "" > > | #define PACKAGE_STRING "" > > | #define PACKAGE_BUGREPORT "" > > | #define PACKAGE "N3" > > | #define VERSION "1.07" > > | #ifdef __cplusplus > > | extern "C" void std::exit (int) throw (); using std::exit; > > | #endif > > | #define HAVE_BLAS 1 > > | #define HAVE_LAPACK 1 > > | /* end confdefs.h. */ > > | #include > > | #ifdef F77_DUMMY_MAIN > > | > > | # ifdef __cplusplus > > | extern "C" > > | # endif > > | int F77_DUMMY_MAIN() { return 1; } > > | > > | #endif > > | int > > | main () > > | { > > | int i = ncopen("",0); > > | ; > > | return 0; > > | } > > configure:6897: result: no > > configure:6900: error: cannot find required library netcdf > > > > > > > > I was wondering why it complains about netcdf.h where it is already > > installed in the correct location? > > > > Thanks, > > > > Siamak > > > > > > > > From minc-users@bic.mni.mcgill.ca Fri Dec 12 14:47:16 2003 From: minc-users@bic.mni.mcgill.ca (Andrew Janke) Date: Fri, 12 Dec 2003 09:47:16 -0500 Subject: [MINC-users] installation problem with N3 on Linux (red hat 9) In-Reply-To: <002c01c3c088$ad03d2a0$2f6363c0@itmedicine.net> Message-ID: On Fri, 12 Dec 2003, siamak ardekani wrote: > Thanks again for the comment. Finally, I was able install N3 and make it > run. To test the performance I tried to run nu_correct on one of the data > files located in the N3/testing folder named block.mnc. However, I didn't > see any difference before and after correction. I also ran the program on a > real MRI brain data without any success (using different combinations > of -stop, -distance, -iteration and -fwhm). Is there any appropriate way to > check the algorithm and make sure that installation has been done ok. John Sled (the Author of N3) is really the one who should comment here but... The variations in intensity that N3 removes are often very subtle, and often subtle enough that the eye cannot pick them out without a bit of "help". To see if there really is any difference between the images do this: $ mincdiff input.mnc output.mnc If there are differences (apart from the header) reported continue to something like this: $ mincmath -sub input.mnc output.mnc diff.mnc $ register input.mnc diff.mnc -- Andrew Janke ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3365 4100 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From minc-users@bic.mni.mcgill.ca Fri Dec 12 16:29:10 2003 From: minc-users@bic.mni.mcgill.ca (John G. Sled) Date: Fri, 12 Dec 2003 10:29:10 -0600 Subject: [MINC-users] installation problem with N3 on Linux (red hat 9) In-Reply-To: References: <002c01c3c088$ad03d2a0$2f6363c0@itmedicine.net> Message-ID: <20031212162910.GA4488@sickkids.ca> I have a couple of comments to add. N3 comes with a test suite that can be run with the 'make test' command. This should verify that the volumes are being corrected. Also, for any given correction, one can generate the field estimate as follows nu_correct input.mnc output.mnc imp2field -like output.mnc output.imp output_field.mnc This is easier than dividing the output by the input and contending with division by zero issues. John On Fri, Dec 12, 2003 at 09:47:16AM -0500, Andrew Janke wrote: > On Fri, 12 Dec 2003, siamak ardekani wrote: > > > Thanks again for the comment. Finally, I was able install N3 and make it > > run. To test the performance I tried to run nu_correct on one of the data > > files located in the N3/testing folder named block.mnc. However, I didn't > > see any difference before and after correction. I also ran the program on a > > real MRI brain data without any success (using different combinations > > of -stop, -distance, -iteration and -fwhm). Is there any appropriate way to > > check the algorithm and make sure that installation has been done ok. > > John Sled (the Author of N3) is really the one who should comment here but... > > The variations in intensity that N3 removes are often very subtle, and often > subtle enough that the eye cannot pick them out without a bit of "help". > > To see if there really is any difference between the images do this: > > $ mincdiff input.mnc output.mnc > > If there are differences (apart from the header) reported continue to something > like this: > > $ mincmath -sub input.mnc output.mnc diff.mnc > $ register input.mnc diff.mnc > > -- > Andrew Janke ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) > Australia->University of Queensland->Centre for Magnetic Resonance > W: +61 7 3365 4100 || H: +61 7 3800 4042 || M: +61 4 2138 8581 > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From mdesco@cim.mcgill.ca Sat Dec 13 21:08:24 2003 From: mdesco@cim.mcgill.ca (Maxime Descoteaux) Date: Sat, 13 Dec 2003 16:08:24 -0500 (EST) Subject: [MINC-users] voxel_loop problem Message-ID: <34875.132.206.73.105.1071349704.squirrel@www.cim.mcgill.ca> Hi, I now understand how to set things up but I get weird things happening. If I construct the simplest example possible, I copy an existing file to another using voxel_loop. char *in_files[] = {"image.mnc"}; char *out_files[] = {"out.mnc"}; int num_in = 1; int num_out = 1; voxel_loop(num_in, in_files, num_out, out_files, NULL, NULL, identity_function, NULL); void identity_function(...) { long ivox, num_values; num_values = num_voxels * input_vector_length; for(ivox = 0; ivox < num_values; ivox++) { output_data[0][ivox] = input_data[0][ivox]; print("%f\n", output_data[0][ivox]); } } Problem: The printout of the values is all over the place... I get values of order 1.27e+308. Anyways, the values are not at all matching the image.mnc values. However, if I display out.mnc, both image are the same???? What is going on here? YOu can easily imagine that when I try to do anything interesting with the values things BLOW up. Can you help me? Maxime -- Maxime Descoteaux phone: (514) 989-8670 Centre for Intelligent Machines phone: (514) 398-5606 Masters in Computer Science McGill University http://www.cim.mcgill.ca/~mdesco From minc-users@bic.mni.mcgill.ca Sun Dec 14 00:02:49 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Sat, 13 Dec 2003 19:02:49 -0500 (EST) Subject: [MINC-users] N3 nu_correct crashed Message-ID: Hi All, When I run the nu_correct after compiled N3 package for RedHat 9, I got this: $ nu_correct input.mnc.gz output.mnc expected floating-point argument for "-const" but got"DEBUG: state of _s: 0 DEBUG: state of _s: 0 DEBUG: state of path: /tmp/test DEBUG: state of _s: 0 2.96985e-15" Usage: /usr/local/mni/bin/mincmath [options] [ ...] /usr/local/mni/bin/mincmath -help nu_estimate_np_and_em: crashed while running mincmath (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=2 -- Andre Matos amatos@mrs.mni.mcgill.ca From minc-users@bic.mni.mcgill.ca Sun Dec 14 00:30:18 2003 From: minc-users@bic.mni.mcgill.ca (siamak ardekani) Date: Sat, 13 Dec 2003 16:30:18 -0800 Subject: [MINC-users] N3 nu_correct crashed References: Message-ID: <004701c3c1d9$799bbf20$2f6363c0@itmedicine.net> Is there any particular reason for using a compressed input file (input.mnc.gz) instead of (input.mnc)? Siamak ----- Original Message ----- From: "Andre MATOS" To: "MINC-users" Sent: Saturday, December 13, 2003 4:02 PM Subject: [MINC-users] N3 nu_correct crashed > Hi All, > > When I run the nu_correct after compiled N3 package for RedHat 9, I got > this: > > $ nu_correct input.mnc.gz output.mnc > > expected floating-point argument for "-const" but got"DEBUG: state of _s: > 0 > DEBUG: state of _s: 0 > DEBUG: state of path: /tmp/test > DEBUG: state of _s: 0 > 2.96985e-15" > > Usage: /usr/local/mni/bin/mincmath [options] [ ...] > /usr/local/mni/bin/mincmath -help > > nu_estimate_np_and_em: crashed while running mincmath (termination > status=256) > nu_correct: crashed while running nu_estimate_np_and_em (termination > status=2 > > > > -- > Andre Matos > amatos@mrs.mni.mcgill.ca > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From minc-users@bic.mni.mcgill.ca Sun Dec 14 00:35:32 2003 From: minc-users@bic.mni.mcgill.ca (Steve ROBBINS) Date: Sat, 13 Dec 2003 19:35:32 -0500 Subject: [MINC-users] N3 nu_correct crashed In-Reply-To: ; from amatos@mrs.mni.mcgill.ca on Sat, Dec 13, 2003 at 07:02:49PM -0500 References: Message-ID: <20031213193532.B666877@shadow.bic.mni.mcgill.ca> On Sat, Dec 13, 2003 at 07:02:49PM -0500, Andre MATOS wrote: > $ nu_correct input.mnc.gz output.mnc > > expected floating-point argument for "-const" but got"DEBUG: state of _s: > 0 > DEBUG: state of _s: 0 > DEBUG: state of path: /tmp/test > DEBUG: state of _s: 0 > 2.96985e-15" Unfortunately, EBTKS 1.0 had some debugging code left in that should not have been. Please download & install EBTKS 1.1, then rebuild N3. For future reference, I've collected the errata for the MINC 1.2 CD release on the following page. http://www.bic.mni.mcgill.ca/~stever/Software/RelNotes/CD-minc-1.2.html Regards, -Steve From minc-users@bic.mni.mcgill.ca Sun Dec 14 14:58:13 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Sun, 14 Dec 2003 09:58:13 -0500 (EST) Subject: [MINC-users] N3 nu_correct crashed In-Reply-To: <20031213193532.B666877@shadow.bic.mni.mcgill.ca> Message-ID: Hi Steve, I got the version 1.1 of EBTKS and also the version 1.07 of N3. Now it's working here in my PC with Linux Red Hat 9. Lets move to next steps: Display, Register and XDisp. Thanks. Andre download On Sat, 13 Dec 2003, Steve ROBBINS wrote: > On Sat, Dec 13, 2003 at 07:02:49PM -0500, Andre MATOS wrote: > > $ nu_correct input.mnc.gz output.mnc > > > > expected floating-point argument for "-const" but got"DEBUG: state of _s: > > 0 > > DEBUG: state of _s: 0 > > DEBUG: state of path: /tmp/test > > DEBUG: state of _s: 0 > > 2.96985e-15" > > Unfortunately, EBTKS 1.0 had some debugging code left in that > should not have been. Please download & install EBTKS 1.1, > then rebuild N3. > > For future reference, I've collected the errata for the MINC 1.2 > CD release on the following page. > > http://www.bic.mni.mcgill.ca/~stever/Software/RelNotes/CD-minc-1.2.html > > > Regards, > -Steve > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andre Matos amatos@mrs.mni.mcgill.ca From minc-users@bic.mni.mcgill.ca Sun Dec 14 15:29:44 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Sun, 14 Dec 2003 10:29:44 -0500 (EST) Subject: [MINC-users] Problems to compile and install Register and Display In-Reply-To: <20030813135417.A5323@shadow.bic.mni.mcgill.ca> Message-ID: Hi Steve, I don't know if you remember the problem that we worked arround when I tried to compile Display and Register into my Linux Red Hat 9 at home. At that time, I had a problem with GL/Glut lib and we did some steps to go around and avoid installing the library to get compiled the tools. The question is: Do I need to install the GL/Glut? I got the Display version 1.3.7 and the Register 1.3.3 and when I try to compile I got this: checking for GL/glut.h... no configure: error: cannot find required header and when I checked the config.log, I saw this: configure:22315: checking GL/glut.h presence configure:22325: /usr/bin/cc -E -Df2cFortran -DNDEBUG -I/usr/local/mni/include conftest.c conftest.c:32:21: GL/glut.h: No such file or directory Thanks. -- Andre Matos amatos@mrs.mni.mcgill.ca From mdesco@cim.mcgill.ca Mon Dec 15 14:22:33 2003 From: mdesco@cim.mcgill.ca (Maxime Descoteaux) Date: Mon, 15 Dec 2003 09:22:33 -0500 (EST) Subject: [MINC-users] quick voxel loop question Message-ID: <35081.132.206.73.105.1071498153.squirrel@www.cim.mcgill.ca> Hi all, I fixed my previous email's problem. Quick question about file I/O.... Can we give an option to overwrite files when using voxel_loop. Right now, if a file already exists in my list of output files, nccreate sends an error message: nccreate: filename "/tmp/max/vesselness.mnc": File exists micreate: MINC package entry point Thanks -- Maxime Descoteaux phone: (514) 989-8670 Centre for Intelligent Machines phone: (514) 398-5606 Masters in Computer Science McGill University http://www.cim.mcgill.ca/~mdesco From minc-users@bic.mni.mcgill.ca Mon Dec 15 15:47:13 2003 From: minc-users@bic.mni.mcgill.ca (Andrew Janke) Date: Mon, 15 Dec 2003 10:47:13 -0500 Subject: [MINC-users] quick voxel loop question In-Reply-To: <35081.132.206.73.105.1071498153.squirrel@www.cim.mcgill.ca> Message-ID: On Mon, 15 Dec 2003, Maxime Descoteaux wrote: > Quick question about file I/O.... > Can we give an option to overwrite files when using voxel_loop. Right > now, if a file already exists in my list of output files, nccreate sends > an error message: > > nccreate: filename "/tmp/max/vesselness.mnc": File exists > micreate: MINC package entry point You need to set a "clobber" option. set_loop_clobber(loop_opts, TRUE); -- Andrew Janke ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3365 4100 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From minc-users@bic.mni.mcgill.ca Sun Dec 14 00:44:41 2003 From: minc-users@bic.mni.mcgill.ca (Paul Thompson) Date: Sat, 13 Dec 2003 16:44:41 -0800 Subject: [MINC-users] N3 nu_correct crashed In-Reply-To: <004701c3c1d9$799bbf20$2f6363c0@itmedicine.net> Message-ID: Hi Siamak, It will just read the input file faster if it's compressed, but it won't affect the result. Most of the MINC tools that call volume I/O are designed to read inputs that are gzipped, which is quite nice as it avoids filling drives with giant files. :) See you, Paul http://www.loni.ucla.edu/~thompson/thompson.html On Saturday, December 13, 2003, at 04:30 PM, siamak ardekani wrote: > > Is there any particular reason for using a compressed input file > (input.mnc.gz) instead of (input.mnc)? > > Siamak > > > ----- Original Message ----- > From: "Andre MATOS" > To: "MINC-users" > Sent: Saturday, December 13, 2003 4:02 PM > Subject: [MINC-users] N3 nu_correct crashed > > >> Hi All, >> >> When I run the nu_correct after compiled N3 package for RedHat 9, I >> got >> this: >> >> $ nu_correct input.mnc.gz output.mnc >> >> expected floating-point argument for "-const" but got"DEBUG: state of >> _s: >> 0 >> DEBUG: state of _s: 0 >> DEBUG: state of path: /tmp/test >> DEBUG: state of _s: 0 >> 2.96985e-15" >> >> Usage: /usr/local/mni/bin/mincmath [options] [ ...] >> /usr/local/mni/bin/mincmath -help >> >> nu_estimate_np_and_em: crashed while running mincmath (termination >> status=256) >> nu_correct: crashed while running nu_estimate_np_and_em (termination >> status=2 >> >> >> >> -- >> Andre Matos >> amatos@mrs.mni.mcgill.ca >> >> >> _______________________________________________ >> MINC-users@bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From minc-users@bic.mni.mcgill.ca Mon Dec 15 16:50:48 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Mon, 15 Dec 2003 11:50:48 -0500 (EST) Subject: [MINC-users] mritotal freezes Message-ID: Hi, I installed the mni_autoreg and when I run mritotal my Linux Red Hat 9 freezes. I tried to use the options "-verbose" and also "-debug" to see messages, but the mritotal didn't wrote any output, just freeze. The others tools such as mritoself is working perfect. Does anyone have any idea? Thanks. -- Andre Matos amatos@mrs.mni.mcgill.ca From mdesco@cim.mcgill.ca Mon Dec 15 18:44:28 2003 From: mdesco@cim.mcgill.ca (Maxime Descoteaux) Date: Mon, 15 Dec 2003 13:44:28 -0500 (EST) Subject: [MINC-users] killed Message-ID: <35205.132.206.73.105.1071513868.squirrel@www.cim.mcgill.ca> Hey, My MINC program gets "killed" after a few minutes of computation. Before, I thought I was running out of memory but I have recently implemented all my stuff with voxel loop and still, I get a "killed". Now, the only difference is that I get it much later in the computation. What could cause that "killed"? Thanks -- Maxime Descoteaux phone: (514) 989-8670 Centre for Intelligent Machines phone: (514) 398-5606 Masters in Computer Science McGill University http://www.cim.mcgill.ca/~mdesco From minc-users@bic.mni.mcgill.ca Tue Dec 16 21:55:25 2003 From: minc-users@bic.mni.mcgill.ca (minc-users@bic.mni.mcgill.ca) Date: Tue, 16 Dec 2003 16:55:25 -0500 (EST) Subject: [MINC-users] Re: Problems to compile and install Register and Display Message-ID: Andre, I just did a new install of netcdf, bicpl, minc, and Register on Redhat 9. Thanks for your post on Oct 24th. That saved me a lot of time. With the Register install, I ran into some of the same problems that you have. I believe the glut.h file is included in the glut-devel rpm: [root@radium Register-1.3.3]# rpm -qf /usr/include/GL/glut.h glut-devel-3.7-12 I also encountered the problem you posted way back on Aug 13: > > checking for GL/glut.h... yes > > checking for glutInit in -lglut... no > > configure: error: cannot find required library I found one possible work around for this was to define: export X_LIBS=-lXi before running configure. hope some of this is helpful, -Adam Thomas From minc-users@bic.mni.mcgill.ca Wed Dec 17 03:31:20 2003 From: minc-users@bic.mni.mcgill.ca (Peter NEELIN) Date: Tue, 16 Dec 2003 22:31:20 -0500 Subject: [MINC-users] killed In-Reply-To: <35205.132.206.73.105.1071513868.squirrel@www.cim.mcgill.ca> Message-ID: On Mon, 15 Dec 2003, Maxime Descoteaux wrote: > My MINC program gets "killed" after a few minutes of computation. Before, > I thought I was running out of memory but I have recently implemented all > my stuff with voxel loop and still, I get a "killed". Now, the only > difference is that I get it much later in the computation. That usually means that the system has run out of memory and has selected your process to be killed. Check the system log file, if you can - it should give more detail. Without knowing more about the system on which you are running the program, or more about the program it is hard to advise. But it is unlikely that a well-behaved voxel-loop program would run out of memory part way through since it allocates its buffers at the beginning. Is it possible that your computation code has a memory leak? Try monitoring the process size with top or ps. Peter ---- Peter Neelin (neelin@bic.mni.mcgill.ca) From minc-users@bic.mni.mcgill.ca Wed Dec 17 14:33:45 2003 From: minc-users@bic.mni.mcgill.ca (Andrew Janke) Date: Wed, 17 Dec 2003 09:33:45 -0500 Subject: [MINC-users] mritotal freezes In-Reply-To: Message-ID: On Mon, 15 Dec 2003, Andre MATOS wrote: > I installed the mni_autoreg and when I run mritotal > my Linux Red Hat 9 freezes. I tried to use the options "-verbose" and also > "-debug" to see messages, but the mritotal didn't wrote any output, just > freeze. > > The others tools such as mritoself is working perfect. This on surface value appears very strange (as mritotal and mritoself are very similar -- both perl scripts that both call other MINC programs) However a few questions.. 1. When you say redhat "freezes" does just the window you run mritotal in freeze or does the whole computer freeze up? 2. Is there any output with mritotal -noexecute -debug -verbose ? or with mritotal -version ? -- Andrew Janke ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3365 4100 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From minc-users@bic.mni.mcgill.ca Wed Dec 17 16:03:22 2003 From: minc-users@bic.mni.mcgill.ca (John G. Sled) Date: Wed, 17 Dec 2003 10:03:22 -0600 Subject: [MINC-users] mritotal freezes In-Reply-To: References: Message-ID: <20031217160322.GA5938@sickkids.ca> I have had a similar problem with mritotal on Redhat 9 that seemed to be an issue with unicode characters and perl. Try setting the environment variable LANG=C before running mritotal. John On Wed, Dec 17, 2003 at 09:33:45AM -0500, Andrew Janke wrote: > On Mon, 15 Dec 2003, Andre MATOS wrote: > > > I installed the mni_autoreg and when I run mritotal > > my Linux Red Hat 9 freezes. I tried to use the options "-verbose" and also > > "-debug" to see messages, but the mritotal didn't wrote any output, just > > freeze. > > > > The others tools such as mritoself is working perfect. > > This on surface value appears very strange (as mritotal and mritoself are very > similar -- both perl scripts that both call other MINC programs) > > However a few questions.. > > 1. When you say redhat "freezes" does just the window you run mritotal in > freeze or does the whole computer freeze up? > > 2. Is there any output with mritotal -noexecute -debug -verbose ? > or with mritotal -version ? > > > -- > Andrew Janke ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) > Australia->University of Queensland->Centre for Magnetic Resonance > W: +61 7 3365 4100 || H: +61 7 3800 4042 || M: +61 4 2138 8581 > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From minc-users@bic.mni.mcgill.ca Thu Dec 18 20:54:47 2003 From: minc-users@bic.mni.mcgill.ca (Akemi Tomoda) Date: Thu, 18 Dec 2003 15:54:47 -0500 Subject: [MINC-users] talairach transform Message-ID: This is a multi-part message in MIME format... ------------=_1071780983-20567-381 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Content-Disposition: inline Hello list, Please bear with me for such rudimentary questions. During these couple of months, I have been trying to deal with the FreeSurfer study to measure the brain cortex morphometricaly. However, I am having trouble with automatic cutting planes so need to know more about the Talairach transform since I have 2 major reasons. 1) 60% of our samples failed at the end of stage one because FS could not find a cutting plane. I'm still in the process of investigating this As far as I know, the optimized sample (bert) data has the seed point being chosen well, but I should manually select a seed point. 2) There is a significant difference between succeeded and unsucceeded groups (P<0.05). The brain size of succeeded group (n=5); 1662.78+31.98 cm3, on the other hand, the brain size of unsucceeded group (n=7); 1433.15+191.26 cm3. So I guess, the skull size, rather to say, the brain size should be investigated more precisely, since I am dealing with pediatric samples. Assuming the talairach is good, the manual gives a procedure for defining the cutting planes. I am used to running all the processing from the command line using recon-all. Is there a way to set the callosum point and pontine point and still use the command line, or do I have to use the GUI in if I want to do a manual cut? Please let me know your idea at your earliest convenience. In addition, I also would like to get hold of Dave MacDonalds surface extraction stuff from the MNI. Please let me know how I can contact with them. With warmest personal regards, Akemi Tomoda Developmental Biopsychiatry Research Program McLean Hospital of Harvard Medical School atomoda@mclean.harvard.edu Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer. ------------=_1071780983-20567-381-- From minc-users@bic.mni.mcgill.ca Fri Dec 19 19:36:07 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Fri, 19 Dec 2003 14:36:07 -0500 (EST) Subject: [MINC-users] Problem to install mni_perl and Getopt-Tabular Message-ID: Hi, I am trying to install all packages (NetCDF, Minc, BicPL, mni_perl, EBTKS, CLAPACK, Getopt-Tabular, N3, mni_autoreg, and mni_autoreg-model) into a temporality directory (I don't have root rights and also I don't want to kill the old version that I have). I didn't have problem with NetCDF, Minc, BicPL, EBTKS, CLAPACK and N3. However, mni_autoreg requires mni_perl and Getopt-Tabular to be compiled. And here is the question: before I used this to change the directory: ./configure --prefix=/temporality/local but for mni-perl and Getopt-Tabular I used this: perl Makefile.PL PREFIX=/temporality/local/ INSTALLDIRS=perl However, when I try to compile mni_autoreg it fails. It seems that the mni_autoreg can not find the perl libs that is necessary. Does anyone know how to get around this problem? Thanks. -- Andre Matos amatos@mrs.mni.mcgill.ca From minc-users@bic.mni.mcgill.ca Fri Dec 19 19:43:55 2003 From: minc-users@bic.mni.mcgill.ca (Andrew Janke) Date: Fri, 19 Dec 2003 14:43:55 -0500 Subject: [MINC-users] Problem to install mni_perl and Getopt-Tabular In-Reply-To: Message-ID: On Fri, 19 Dec 2003, Andre MATOS wrote: > I didn't have problem with NetCDF, Minc, BicPL, EBTKS, CLAPACK and N3. > However, mni_autoreg requires mni_perl and Getopt-Tabular to be compiled. > And here is the question: before I used this to change the directory: > > ./configure --prefix=/temporality/local > > but for mni-perl and Getopt-Tabular I used this: > > perl Makefile.PL PREFIX=/temporality/local/ INSTALLDIRS=perl > > However, when I try to compile mni_autoreg it fails. It seems that the > mni_autoreg can not find the perl libs that is necessary. Did you also specify a --with-build-path=/temporality/local ? -- Andrew Janke ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3365 4100 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From minc-users@bic.mni.mcgill.ca Fri Dec 19 19:53:18 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Fri, 19 Dec 2003 14:53:18 -0500 (EST) Subject: [MINC-users] Problem to install mni_perl and Getopt-Tabular In-Reply-To: Message-ID: Yes Andrew. On Fri, 19 Dec 2003, Andrew Janke wrote: > On Fri, 19 Dec 2003, Andre MATOS wrote: > > > I didn't have problem with NetCDF, Minc, BicPL, EBTKS, CLAPACK and N3. > > However, mni_autoreg requires mni_perl and Getopt-Tabular to be compiled. > > And here is the question: before I used this to change the directory: > > > > ./configure --prefix=/temporality/local > > > > but for mni-perl and Getopt-Tabular I used this: > > > > perl Makefile.PL PREFIX=/temporality/local/ INSTALLDIRS=perl > > > > However, when I try to compile mni_autoreg it fails. It seems that the > > mni_autoreg can not find the perl libs that is necessary. > > Did you also specify a --with-build-path=/temporality/local ? > > -- > Andrew Janke ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) > Australia->University of Queensland->Centre for Magnetic Resonance > W: +61 7 3365 4100 || H: +61 7 3800 4042 || M: +61 4 2138 8581 > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andre Matos amatos@mrs.mni.mcgill.ca From minc-users@bic.mni.mcgill.ca Fri Dec 19 20:01:15 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Fri, 19 Dec 2003 15:01:15 -0500 (EST) Subject: [MINC-users] Problem to install mni_perl and Getopt-Tabular In-Reply-To: Message-ID: Yes Andrew, I did. What about the PERLLIB environment variable. My is setting: PERLLIB=/usr/local/mni/lib/perl5 Thanks > > > On Fri, 19 Dec 2003, Andrew Janke wrote: > > > On Fri, 19 Dec 2003, Andre MATOS wrote: > > > > > I didn't have problem with NetCDF, Minc, BicPL, EBTKS, CLAPACK and N3. > > > However, mni_autoreg requires mni_perl and Getopt-Tabular to be compiled. > > > And here is the question: before I used this to change the directory: > > > > > > ./configure --prefix=/temporality/local > > > > > > but for mni-perl and Getopt-Tabular I used this: > > > > > > perl Makefile.PL PREFIX=/temporality/local/ INSTALLDIRS=perl > > > > > > However, when I try to compile mni_autoreg it fails. It seems that the > > > mni_autoreg can not find the perl libs that is necessary. > > > > Did you also specify a --with-build-path=/temporality/local ? > > > > -- > > Andrew Janke ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) > > Australia->University of Queensland->Centre for Magnetic Resonance > > W: +61 7 3365 4100 || H: +61 7 3800 4042 || M: +61 4 2138 8581 > > > > _______________________________________________ > > MINC-users@bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > -- Andre Matos amatos@mrs.mni.mcgill.ca From minc-users@bic.mni.mcgill.ca Fri Dec 19 20:06:22 2003 From: minc-users@bic.mni.mcgill.ca (Jason Lerch) Date: Fri, 19 Dec 2003 15:06:22 -0500 Subject: [MINC-users] Problem to install mni_perl and Getopt-Tabular In-Reply-To: References: Message-ID: Set your PERL5LIB environment variable to reflect where you installed the perl libraries. Hope this helps, Jason On Dec 19, 2003, at 2:53 PM, Andre MATOS wrote: > Yes Andrew. > > > On Fri, 19 Dec 2003, Andrew Janke wrote: > >> On Fri, 19 Dec 2003, Andre MATOS wrote: >> >>> I didn't have problem with NetCDF, Minc, BicPL, EBTKS, CLAPACK and >>> N3. >>> However, mni_autoreg requires mni_perl and Getopt-Tabular to be >>> compiled. >>> And here is the question: before I used this to change the directory: >>> >>> ./configure --prefix=/temporality/local >>> >>> but for mni-perl and Getopt-Tabular I used this: >>> >>> perl Makefile.PL PREFIX=/temporality/local/ INSTALLDIRS=perl >>> >>> However, when I try to compile mni_autoreg it fails. It seems that >>> the >>> mni_autoreg can not find the perl libs that is necessary. >> >> Did you also specify a --with-build-path=/temporality/local ? >> >> -- >> Andrew Janke ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) >> Australia->University of Queensland->Centre for Magnetic Resonance >> W: +61 7 3365 4100 || H: +61 7 3800 4042 || M: +61 4 2138 8581 >> >> _______________________________________________ >> MINC-users@bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > -- > Andre Matos > amatos@mrs.mni.mcgill.ca > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From minc-users@bic.mni.mcgill.ca Fri Dec 19 20:53:37 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Fri, 19 Dec 2003 15:53:37 -0500 (EST) Subject: [MINC-users] mni_autoreg compilation failed Message-ID: Hi, I got this error when I was compiling the mni_autoreg-0.98k: make[3]: Entering directory `/scratch/amatos/local/mni_source/mni_autoreg-0.98k/minctracc/Optimize' if gcc -DHAVE_CONFIG_H -I. -I. -I../.. -I./../Include -I../../Proglib -Df2cFortran -DNDEBUG -I/scratch/amatos/local/mni/include -O -MT optimize.o -MD -MP -MF ".deps/optimize.Tpo" \ -c -o optimize.o `test -f 'optimize.c' || echo './'`optimize.c; \ then mv -f ".deps/optimize.Tpo" ".deps/optimize.Po"; \ else rm -f ".deps/optimize.Tpo"; exit 1; \ fi optimize.c: In function `optimize_linear_transformation': optimize.c:732: parse error before `void' make[3]: *** [optimize.o] Error 1 make[3]: Leaving directory `/scratch/amatos/local/mni_source/mni_autoreg-0.98k/minctracc/Optimize' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/scratch/amatos/local/mni_source/mni_autoreg-0.98k/minctracc' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/scratch/amatos/local/mni_source/mni_autoreg-0.98k' make: *** [all] Error 2 Is this related to any required lib? Thanks. -- Andre Matos amatos@mrs.mni.mcgill.ca From minc-users@bic.mni.mcgill.ca Sat Dec 20 12:06:25 2003 From: minc-users@bic.mni.mcgill.ca (Steve ROBBINS) Date: Sat, 20 Dec 2003 07:06:25 -0500 Subject: [MINC-users] Problem to install mni_perl and Getopt-Tabular In-Reply-To: ; from amatos@mrs.mni.mcgill.ca on Fri, Dec 19, 2003 at 02:36:07PM -0500 References: Message-ID: <20031220070625.B1044432@shadow.bic.mni.mcgill.ca> On Fri, Dec 19, 2003 at 02:36:07PM -0500, Andre MATOS wrote: > However, mni_autoreg requires mni_perl and Getopt-Tabular to be compiled. Actually, mni_autoreg does not require mni perllib, notwithstanding the web page (http://www.bic.mni.mcgill.ca/software/distribution/). > And here is the question: before I used this to change the directory: > > ./configure --prefix=/temporality/local > > but for mni-perl and Getopt-Tabular I used this: > > perl Makefile.PL PREFIX=/temporality/local/ INSTALLDIRS=perl > > However, when I try to compile mni_autoreg it fails. It seems that the > mni_autoreg can not find the perl libs that is necessary. The build per se should work. It does not check that Getopt::Tabular is installed, nor are any of the perl scripts run. Running "make check", on the other hand does run the perl scripts and will fail if Getopt::Tabular is missing. -Steve From minc-users@bic.mni.mcgill.ca Sat Dec 20 12:19:51 2003 From: minc-users@bic.mni.mcgill.ca (Steve ROBBINS) Date: Sat, 20 Dec 2003 07:19:51 -0500 Subject: [MINC-users] mni_autoreg compilation failed In-Reply-To: ; from amatos@mrs.mni.mcgill.ca on Fri, Dec 19, 2003 at 03:53:37PM -0500 References: Message-ID: <20031220071951.C1044432@shadow.bic.mni.mcgill.ca> On Fri, Dec 19, 2003 at 03:53:37PM -0500, Andre MATOS wrote: > Hi, > > I got this error when I was compiling the mni_autoreg-0.98k: > > make[3]: Entering directory > `/scratch/amatos/local/mni_source/mni_autoreg-0.98k/minctracc/Optimize' > if gcc -DHAVE_CONFIG_H -I. -I. -I../.. -I./../Include -I../../Proglib > -Df2cFortran -DNDEBUG -I/scratch/amatos/local/mni/include -O -MT > optimize.o -MD -MP -MF ".deps/optimize.Tpo" \ > -c -o optimize.o `test -f 'optimize.c' || echo './'`optimize.c; \ > then mv -f ".deps/optimize.Tpo" ".deps/optimize.Po"; \ > else rm -f ".deps/optimize.Tpo"; exit 1; \ > fi > optimize.c: In function `optimize_linear_transformation': > optimize.c:732: parse error before `void' > Is this related to any required lib? No. There are two likely possibilities. First, it is possible that your copy of mni_autoreg is corrupted. Try downloading it again and comparing the two copies of optimize.c using diff. The second possibility is that declaring a function in the middle of another function is a nonstandard extension that has been removed. What does "gcc --version" say? Does the following patch fix the problem? --- /home/steve/bicsrc/cvs/registration/mni_autoreg/minctracc/Optimize/optimize.c 2003-07-27 11:30:55.000000000 -0400 +++ minctracc/Optimize/optimize.c 2003-12-20 07:14:00.000000000 -0500 @@ -179,6 +179,10 @@ amoeba_struct *amoeba ); +public void normalize_data_to_match_target(Volume d1, Volume m1, Real thresh1, + Volume d2, Volume m2, Real thresh2, + Arg_Data *globals); + public void make_zscore_volume(Volume d1, Volume m1, Real *threshold); @@ -729,9 +733,6 @@ __FILE__, __LINE__); } -public void normalize_data_to_match_target(Volume d1, Volume m1, Real thresh1, - Volume d2, Volume m2, Real thresh2, - Arg_Data *globals); /* --------------------------------------------------------------*/ /* -------- prepare the weighting array for optimization --------*/ -Steve From minc-users@bic.mni.mcgill.ca Sat Dec 20 14:14:15 2003 From: minc-users@bic.mni.mcgill.ca (Steve ROBBINS) Date: Sat, 20 Dec 2003 09:14:15 -0500 Subject: [MINC-users] Problems to compile and install Register and Display In-Reply-To: ; from amatos@mrs.mni.mcgill.ca on Sun, Dec 14, 2003 at 10:29:44AM -0500 References: <20030813135417.A5323@shadow.bic.mni.mcgill.ca> Message-ID: <20031220091415.E1044432@shadow.bic.mni.mcgill.ca> On Sun, Dec 14, 2003 at 10:29:44AM -0500, Andre MATOS wrote: > Hi Steve, > > I don't know if you remember the problem that we worked arround when I > tried to compile Display and Register into my Linux Red Hat 9 at home. Yes, thanks for reminding me. I have rolled out new releases of Display and Register with the fix. They are now available on the BIC software web page http://www.bic.mni.mcgill.ca/software/distribution/ > At that time, I had a problem with GL/Glut lib and we did some steps to go > around and avoid installing the library to get compiled the tools. > > The question is: Do I need to install the GL/Glut? Yes, you need both GL and glut. The problem with Redhat 9 systems is that you now need to explicitly specify -lXi when linking, as Adam Thomas mentioned here recently. The new register and display packages now do this, so his workaround should not be necessary. (Please let me know if this is incorrect) Cheers, -Steve From minc-users@bic.mni.mcgill.ca Mon Dec 22 16:04:42 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Mon, 22 Dec 2003 11:04:42 -0500 (EST) Subject: [MINC-users] minc 1.2 errors on Mac OS X Message-ID: Hi, After I compiled the mimc version 1.2 into the Mac OS X 10.2.8 without errors, I runned "make check" to be sure that it was compiled ok, but I got this: ... make check-TESTS Testing minc_types Segmentation fault FAIL: run_tests.csh dd: stdout: Broken pipe 33+0 records in 32+0 records out 16384 bytes transferred in 0.063670 secs (257327 bytes/sec) PASS: xfmconcat_01.sh dd: stdout: Broken pipe 33+0 records in 32+0 records out 16384 bytes transferred in 0.062224 secs (263307 bytes/sec) PASS: xfmconcat_02.sh =================== 1 of 3 tests failed =================== make[2]: *** [check-TESTS] Error 1 make[1]: *** [check-am] Error 2 make: *** [check-recursive] Error 1 Is this related with the problem that I got before when I tried to run, for example, mincmath I needed to run gzunzip before run it? Thanks. -- Andre Matos amatos@mrs.mni.mcgill.ca From minc-users@bic.mni.mcgill.ca Mon Dec 22 16:19:06 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Mon, 22 Dec 2003 11:19:06 -0500 (EST) Subject: [MINC-users] Basic question about shared and static Minc libraries Message-ID: Hi Minc Users, Can anyone give me a little explanation about shared and static libraries in the minc tools and in which way should I use each one? checking whether to build shared libraries... no checking whether to build static libraries... yes Thanks!!! -- Andre Matos amatos@mrs.mni.mcgill.ca From minc-users@bic.mni.mcgill.ca Mon Dec 22 18:19:34 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Mon, 22 Dec 2003 13:19:34 -0500 (EST) Subject: [MINC-users] mni_autoreg compilation failed In-Reply-To: <20031220071951.C1044432@shadow.bic.mni.mcgill.ca> Message-ID: Hi Steve The version of the gcc here (Linux Red Hat 7) is 2.96 and the "patch" solved the compilation problem. This is really interesting becouse at home (Linux Red Hat 9) I compilled without errors and without this patch. Do you think that the gcc version could be the problem? I will check late the gcc version that I have at home. Thanks. Andre amatos@mrs.mni.mcgill.ca On Sat, 20 Dec 2003, Steve ROBBINS wrote: > On Fri, Dec 19, 2003 at 03:53:37PM -0500, Andre MATOS wrote: > > Hi, > > > > I got this error when I was compiling the mni_autoreg-0.98k: > > > > make[3]: Entering directory > > `/scratch/amatos/local/mni_source/mni_autoreg-0.98k/minctracc/Optimize' > > if gcc -DHAVE_CONFIG_H -I. -I. -I../.. -I./../Include -I../../Proglib > > -Df2cFortran -DNDEBUG -I/scratch/amatos/local/mni/include -O -MT > > optimize.o -MD -MP -MF ".deps/optimize.Tpo" \ > > -c -o optimize.o `test -f 'optimize.c' || echo './'`optimize.c; \ > > then mv -f ".deps/optimize.Tpo" ".deps/optimize.Po"; \ > > else rm -f ".deps/optimize.Tpo"; exit 1; \ > > fi > > optimize.c: In function `optimize_linear_transformation': > > optimize.c:732: parse error before `void' > > > > Is this related to any required lib? > > No. > > There are two likely possibilities. First, it is possible that your > copy of mni_autoreg is corrupted. Try downloading it again and comparing > the two copies of optimize.c using diff. > > The second possibility is that declaring a function in the middle of > another function is a nonstandard extension that has been removed. > What does "gcc --version" say? Does the following patch fix the problem? > > > --- /home/steve/bicsrc/cvs/registration/mni_autoreg/minctracc/Optimize/optimize.c 2003-07-27 11:30:55.000000000 -0400 > +++ minctracc/Optimize/optimize.c 2003-12-20 07:14:00.000000000 -0500 > @@ -179,6 +179,10 @@ > amoeba_struct *amoeba ); > > > +public void normalize_data_to_match_target(Volume d1, Volume m1, Real thresh1, > + Volume d2, Volume m2, Real thresh2, > + Arg_Data *globals); > + > public void make_zscore_volume(Volume d1, Volume m1, > Real *threshold); > > @@ -729,9 +733,6 @@ > __FILE__, __LINE__); > } > > -public void normalize_data_to_match_target(Volume d1, Volume m1, Real thresh1, > - Volume d2, Volume m2, Real thresh2, > - Arg_Data *globals); > > /* --------------------------------------------------------------*/ > /* -------- prepare the weighting array for optimization --------*/ > > > > -Steve > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andre Matos amatos@mrs.mni.mcgill.ca From minc-users@bic.mni.mcgill.ca Tue Dec 23 03:16:55 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Mon, 22 Dec 2003 22:16:55 -0500 (EST) Subject: [MINC-users] MNI_PERLLIB failed Message-ID: Hi List, when I runned "make test" into the mni_perllib version 0.07, I got the error below. I did these steps: $ wget ftp://ftp.bic.mni.mcgill.ca/pub/minc/mni_perllib-0.07.tar.gz $ tar -xvzf mni_perllib-0.07.tar.gz $ cd mni_perllib-0.07 $ make /usr/local/mni/data $ perl Makefile.PL PREFIX=/usr/local/mni/ INSTALLDIRS=perl $ make $ make test Before runned "make test", when I runned "make" I got the message: Default directory for model data [/usr/local/mni/data]? Checking if your kit is complete... Looks good Makefile.PL: I don't grok the manifypods section, so can't tweak the pod2man args at Makefile.PL line 162. Writing Makefile for mni_perllib [root@pataxo mni_perllib-0.07]# make test rm -f t/datadir.t sed 's|@DEFAULT_DATA_DIR@|/usr/local/mni/data|' t/datadir.t.in > t/datadir.t chmod 444 t/datadir.t rm -f t/toy_ls sed 's|@PERL@|\#!/usr/bin/perl|' t/toy_ls.in > t/toy_ls chmod 555 t/toy_ls PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/batch-0........ok t/batch-1......../usr/bin/getopt: opção inválida -- J /usr/bin/getopt: opção inválida -- Q /usr/bin/getopt: opção inválida -- S /usr/bin/getopt: opção inválida -- s /usr/bin/getopt: opção inválida -- o /usr/bin/getopt: opção inválida -- e batch: error parsing command-line arguments Error closing pipe to batch: at t/batch-1.t line 36 `batch' exited with non-zero status code: 256 at t/batch-1.t line 36 t/batch-1........NOK 1tail: .out29611: Arquivo ou diretório não encontrado /usr/bin/getopt: opção inválida -- J /usr/bin/getopt: opção inválida -- Q /usr/bin/getopt: opção inválida -- S /usr/bin/getopt: opção inválida -- s /usr/bin/getopt: opção inválida -- o /usr/bin/getopt: opção inválida -- e batch: error parsing command-line arguments t/batch-1........dubious Test returned status 0 (wstat 13, 0xd) DIED. FAILED tests 1-21 Failed 21/21 tests, 0.00% okay t/batch-2......../usr/bin/getopt: opção inválida -- J /usr/bin/getopt: opção inválida -- Q /usr/bin/getopt: opção inválida -- l /usr/bin/getopt: opção inválida -- S /usr/bin/getopt: opção inválida -- s /usr/bin/getopt: opção inválida -- o /usr/bin/getopt: opção inválida -- e batch: error parsing command-line arguments t/batch-2........dubious Test returned status 0 (wstat 13, 0xd) DIED. FAILED tests 1-3 Failed 3/3 tests, 0.00% okay t/checkdirs......warning: running test suite as root means not all tests will be run t/checkdirs......FAILED tests 41-42 Failed 2/42 tests, 95.24% okay t/checkfiles.....warning: running test suite as root means not all tests will be run t/checkfiles.....FAILED tests 24-25 Failed 2/41 tests, 95.12% okay t/datadir........ok t/mincutil.......ok 3/22mincutil.t: couldn't find volume_stats; pretending to pass all tests that depend on it t/mincutil.......ok 4/22mincutil.t: couldn't find volume_cog; pretending to pass all tests that depend on it t/mincutil.......ok t/miscutil.......ok t/numutil........ok t/pathutil.......ok t/searchfiles....warning: running test suite as root means not all tests will be run t/searchfiles....ok t/spawn..........FAILED tests 13-15, 19-25 Failed 10/56 tests, 82.14% okay t/startup........ok t/tagset.........ok Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/batch-1.t 0 13 21 21 100.00% 1-21 t/batch-2.t 0 13 3 3 100.00% 1-3 t/checkdirs.t 42 2 4.76% 41-42 t/checkfiles.t 41 2 4.88% 24-25 t/spawn.t 56 10 17.86% 13-15 19-25 Failed 5/14 test scripts, 64.29% okay. 38/381 subtests failed, 90.03% okay. make: ** [test_dynamic] Erro 29 Linux: Red Hat 9 gcc --version gcc (GCC) 3.2.2 20030222 (Red Hat Linux 3.2.2-5) PERL version: perl5 (revision 5.0 version 8 subversion 0) Thanks!!! -- Andre Matos amatos@mrs.mni.mcgill.ca From minc-users@bic.mni.mcgill.ca Tue Dec 23 03:18:40 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Mon, 22 Dec 2003 22:18:40 -0500 (EST) Subject: [MINC-users] mni_autoreg compilation failed In-Reply-To: <20031220071951.C1044432@shadow.bic.mni.mcgill.ca> Message-ID: Hi Steve, the gcc version that I have at home is: gcc (GCC) 3.2.2 20030222 (Red Hat Linux 3.2.2-5) Thanks! Andre amatos@mrs.mni.mcgill.ca On Sat, 20 Dec 2003, Steve ROBBINS wrote: > On Fri, Dec 19, 2003 at 03:53:37PM -0500, Andre MATOS wrote: > > Hi, > > > > I got this error when I was compiling the mni_autoreg-0.98k: > > > > make[3]: Entering directory > > `/scratch/amatos/local/mni_source/mni_autoreg-0.98k/minctracc/Optimize' > > if gcc -DHAVE_CONFIG_H -I. -I. -I../.. -I./../Include -I../../Proglib > > -Df2cFortran -DNDEBUG -I/scratch/amatos/local/mni/include -O -MT > > optimize.o -MD -MP -MF ".deps/optimize.Tpo" \ > > -c -o optimize.o `test -f 'optimize.c' || echo './'`optimize.c; \ > > then mv -f ".deps/optimize.Tpo" ".deps/optimize.Po"; \ > > else rm -f ".deps/optimize.Tpo"; exit 1; \ > > fi > > optimize.c: In function `optimize_linear_transformation': > > optimize.c:732: parse error before `void' > > > > Is this related to any required lib? > > No. > > There are two likely possibilities. First, it is possible that your > copy of mni_autoreg is corrupted. Try downloading it again and comparing > the two copies of optimize.c using diff. > > The second possibility is that declaring a function in the middle of > another function is a nonstandard extension that has been removed. > What does "gcc --version" say? Does the following patch fix the problem? > > > --- /home/steve/bicsrc/cvs/registration/mni_autoreg/minctracc/Optimize/optimize.c 2003-07-27 11:30:55.000000000 -0400 > +++ minctracc/Optimize/optimize.c 2003-12-20 07:14:00.000000000 -0500 > @@ -179,6 +179,10 @@ > amoeba_struct *amoeba ); > > > +public void normalize_data_to_match_target(Volume d1, Volume m1, Real thresh1, > + Volume d2, Volume m2, Real thresh2, > + Arg_Data *globals); > + > public void make_zscore_volume(Volume d1, Volume m1, > Real *threshold); > > @@ -729,9 +733,6 @@ > __FILE__, __LINE__); > } > > -public void normalize_data_to_match_target(Volume d1, Volume m1, Real thresh1, > - Volume d2, Volume m2, Real thresh2, > - Arg_Data *globals); > > /* --------------------------------------------------------------*/ > /* -------- prepare the weighting array for optimization --------*/ > > > > -Steve > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andre Matos amatos@mrs.mni.mcgill.ca