From minc-users@bic.mni.mcgill.ca Thu Aug 7 22:17:58 2003 From: minc-users@bic.mni.mcgill.ca (Yasunari Tosa) Date: Thu, 07 Aug 2003 17:17:58 -0400 Subject: [MINC-users] talairach volume and talairach center Message-ID: <1060291078.4670.13.camel@tosa-nb.nmr.mgh.harvard.edu> Hi, MINC people I'm very confused about the talairach coordinate system and I would appreciate it very much if you could clarify. My question: Where is the talairach origin in the talairached volume? I thought that average_305.mnc is the one aligned with talairach map (the web page says that it can be directly superimposed over the talairach atlas). Thus I thought that this is the "standard" talairached volume. When I did worldtovoxel average_305.mnc 0 0 0 returned non-trivial big values compared with the volume size. 68.25 126.51000000000000512 86.094999999999998863 Here is the MINC linear map stored MINC Linear Transform 1.0000 0.0000 0.0000 -86.0950 0.0000 1.0000 0.0000 -126.5100 0.0000 0.0000 1.0000 -68.2500 0.0000 0.0000 0.0000 1.0000 This means that the average_305 volume center is not the talairach origin. Is this a correct understanding? Thank you. Tosa From minc-users@bic.mni.mcgill.ca Fri Aug 8 12:57:46 2003 From: minc-users@bic.mni.mcgill.ca (CDI HSL - Ressonancia) Date: Fri, 8 Aug 2003 08:57:46 -0300 Subject: [MINC-users] talairach volume and talairach center References: <1060291078.4670.13.camel@tosa-nb.nmr.mgh.harvard.edu> Message-ID: <003801c35da4$48497820$d03384c8@PUCRS.BR> This is a multi-part message in MIME format. ------=_NextPart_000_0035_01C35D8B.22C9E580 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Hi everybody! I´ve been trying to install Display in a Irix 6.5.8 system but the necessary libraries (netcdf, minc, opengl) are not possible to install because there is a missing file called "fec" that should be in the directory /usr/lib32/cmplrs. The configure log file is attatched, maybe it help you to help me. Regards Mauricio ----- Original Message ----- From: Yasunari Tosa To: Sent: Thursday, August 07, 2003 6:17 PM Subject: [MINC-users] talairach volume and talairach center > Hi, MINC people > > I'm very confused about the talairach coordinate system > and I would appreciate it very much if you could clarify. > > My question: > Where is the talairach origin in the talairached volume? > > I thought that average_305.mnc is the one aligned with > talairach map (the web page says that it can be directly > superimposed over the talairach atlas). Thus I thought > that this is the "standard" talairached volume. > > When I did > > worldtovoxel average_305.mnc 0 0 0 > > returned non-trivial big values compared with the volume size. > > 68.25 126.51000000000000512 86.094999999999998863 > > Here is the MINC linear map stored > > MINC Linear Transform > 1.0000 0.0000 0.0000 -86.0950 > 0.0000 1.0000 0.0000 -126.5100 > 0.0000 0.0000 1.0000 -68.2500 > 0.0000 0.0000 0.0000 1.0000 > > This means that the average_305 volume center is not the > talairach origin. > > Is this a correct understanding? > > Thank you. > > Tosa > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > ------=_NextPart_000_0035_01C35D8B.22C9E580 Content-Type: application/octet-stream; name="config.log" Content-Transfer-Encoding: quoted-printable Content-Disposition: attachment; filename="config.log" This file contains any messages produced by compilers while=0A= running configure, to aid debugging if configure makes a mistake.=0A= =0A= configure:928: checking for top-level source-directory=0A= configure:938: checking for m4 preprocessor=0A= configure:945: checking for m4=0A= configure:1012: checking m4 flags=0A= configure:1040: checking for xlc=0A= configure:1085: checking C compiler "c89"=0A= configure:1094: c89 -c -O -DNDEBUG conftest.c 1>&5=0A= No such feature exists (-5,116)=0A= =0A= The MIPSpro C Compiler =0A= (license FEATURE string =3D cc) =0A= requires a license password. =0A= =0A= For license installation and trouble shooting =0A= information visit the web page: =0A= =0A= http://www.sgi.com/Support/Licensing/install_docs.html =0A= =0A= To obtain a Permanent license (proof of purchase=0A= required) or an Evaluation license please=0A= visit our license request web page: =0A= =0A= http://www.sgi.com/Products/license.html =0A= =0A= or send a blank email message to: =0A= =0A= license@sgi.com =0A= =0A= In North America, Silicon Graphics' customers may request =0A= Permanent licenses by sending a facsimile to: =0A= =0A= (650) 932-0537 =0A= =0A= or by calling our technical support hotline =0A= =0A= 1-800-800-4SGI =0A= =0A= If you are Outside of North America or you are not a Silicon =0A= Graphics support customer then contact your local support provider. =0A= =0A= cc-3450 fec: INTERNAL =0A= open_message_catalog: cannot open message catalog file=0A= =0A= =0A= 1 catastrophic error detected in the compilation of "conftest.c".=0A= Compilation aborted.=0A= configure: failed program was:=0A= #line 1087 "configure"=0A= #include "confdefs.h"=0A= =0A= int main() {=0A= =0A= ; return 0; }=0A= configure:1121: checking how to make dependencies=0A= configure:1189: checking for CC=0A= configure:1225: checking C++ compiler "CC"=0A= configure:1243: CC -o conftest -DNDEBUG conftest.C 1>&5=0A= No such feature exists (-5,116)=0A= =0A= The MIPSpro C++ Compiler =0A= (license FEATURE string =3D cpp) =0A= requires a license password. =0A= =0A= For license installation and trouble shooting =0A= information visit the web page: =0A= =0A= http://www.sgi.com/Support/Licensing/install_docs.html =0A= =0A= To obtain a Permanent license (proof of purchase=0A= required) or an Evaluation license please=0A= visit our license request web page: =0A= =0A= http://www.sgi.com/Products/license.html =0A= =0A= or send a blank email message to: =0A= =0A= license@sgi.com =0A= =0A= In North America, Silicon Graphics' customers may request =0A= Permanent licenses by sending a facsimile to: =0A= =0A= (650) 932-0537 =0A= =0A= or by calling our technical support hotline =0A= =0A= 1-800-800-4SGI =0A= =0A= If you are Outside of North America or you are not a Silicon =0A= Graphics support customer then contact your local support provider. =0A= =0A= CC ERROR: cannot exec /usr/lib32/cmplrs/fecc=0A= configure: failed program was:=0A= #line 1230 "configure"=0A= #include "confdefs.h"=0A= #ifdef __cplusplus=0A= extern "C" void exit(int);=0A= #endif=0A= =0A= #include =0A= int main() {=0A= cout << "";=0A= return 0;=0A= }=0A= =0A= configure:1189: checking for cxx=0A= configure:1189: checking for c++=0A= configure:1189: checking for g++=0A= configure:1189: checking for gcc=0A= configure:1294: checking how to run the C preprocessor=0A= configure:1475: checking for f77=0A= configure:1516: f77 -c conftest.f=0A= No such feature exists (-5,116)=0A= =0A= The MIPSpro Fortran 77 Compiler =0A= (license FEATURE string =3D f77) =0A= requires a license password. =0A= =0A= For license installation and trouble shooting =0A= information visit the web page: =0A= =0A= http://www.sgi.com/Support/Licensing/install_docs.html =0A= =0A= To obtain a Permanent license (proof of purchase=0A= required) or an Evaluation license please=0A= visit our license request web page: =0A= =0A= http://www.sgi.com/Products/license.html =0A= =0A= or send a blank email message to: =0A= =0A= license@sgi.com =0A= =0A= In North America, Silicon Graphics' customers may request =0A= Permanent licenses by sending a facsimile to: =0A= =0A= (650) 932-0537 =0A= =0A= or by calling our technical support hotline =0A= =0A= 1-800-800-4SGI =0A= =0A= If you are Outside of North America or you are not a Silicon =0A= Graphics support customer then contact your local support provider. =0A= =0A= f77 ERROR: cannot exec /usr/lib32/cmplrs/mfef77=0A= configure:1548: checking for Fortran .F compiler=0A= configure:1589: checking for Fortran preprocessor=0A= configure:1669: checking for xlf90=0A= configure:1669: checking for f90=0A= configure:1700: checking Fortran-90 compiler "f90"=0A= configure:1702: f90 -o conftest conftest.f90 =0A= No such feature exists (-5,116)=0A= =0A= The MIPSpro Fortran 90 Compiler =0A= (license FEATURE string =3D f90) =0A= requires a license password. =0A= =0A= For license installation and trouble shooting =0A= information visit the web page: =0A= =0A= http://www.sgi.com/Support/Licensing/install_docs.html =0A= =0A= To obtain a Permanent license (proof of purchase=0A= required) or an Evaluation license please=0A= visit our license request web page: =0A= =0A= http://www.sgi.com/Products/license.html =0A= =0A= or send a blank email message to: =0A= =0A= license@sgi.com =0A= =0A= In North America, Silicon Graphics' customers may request =0A= Permanent licenses by sending a facsimile to: =0A= =0A= (650) 932-0537 =0A= =0A= or by calling our technical support hotline =0A= =0A= 1-800-800-4SGI =0A= =0A= If you are Outside of North America or you are not a Silicon =0A= Graphics support customer then contact your local support provider. =0A= =0A= f90 ERROR: cannot exec /usr/lib32/cmplrs/mfef90=0A= configure:1751: checking for nm utility=0A= configure:1758: checking for nm=0A= configure:1825: checking nm flags=0A= configure:2462: checking for math library=0A= configure:2466: checking for tanh in -lc=0A= configure:2504: checking for tanh in -lm=0A= configure:2555: checking for ar utility=0A= configure:2562: checking for ar=0A= configure:2629: checking ar flags=0A= configure:2638: checking for nm utility=0A= configure:2680: checking for nm=0A= configure:2712: checking nm flags=0A= configure:2722: checking for ranlib=0A= configure:2751: checking for stdlib.h=0A= configure:2788: checking for sys/types.h=0A= configure:2824: checking for strerror=0A= configure:2877: checking for working ftruncate()=0A= configure:2930: c89 -o conftest -O -DNDEBUG conftest.c 1>&5=0A= No such feature exists (-5,116)=0A= =0A= The MIPSpro C Compiler =0A= (license FEATURE string =3D cc) =0A= requires a license password. =0A= =0A= For license installation and trouble shooting =0A= information visit the web page: =0A= =0A= http://www.sgi.com/Support/Licensing/install_docs.html =0A= =0A= To obtain a Permanent license (proof of purchase=0A= required) or an Evaluation license please=0A= visit our license request web page: =0A= =0A= http://www.sgi.com/Products/license.html =0A= =0A= or send a blank email message to: =0A= =0A= license@sgi.com =0A= =0A= In North America, Silicon Graphics' customers may request =0A= Permanent licenses by sending a facsimile to: =0A= =0A= (650) 932-0537 =0A= =0A= or by calling our technical support hotline =0A= =0A= 1-800-800-4SGI =0A= =0A= If you are Outside of North America or you are not a Silicon =0A= Graphics support customer then contact your local support provider. =0A= =0A= cc-3450 fec: INTERNAL =0A= open_message_catalog: cannot open message catalog file=0A= =0A= =0A= 1 catastrophic error detected in the compilation of "conftest.c".=0A= Compilation aborted.=0A= configure: failed program was:=0A= #line 2882 "configure"=0A= #include "confdefs.h"=0A= #include =0A= #include =0A= #include =0A= #include =0A= #include =0A= main()=0A= {=0A= char* path =3D tmpnam(NULL);=0A= int exitStatus =3D 1;=0A= =0A= if (path !=3D NULL)=0A= {=0A= int fd =3D open(path, O_RDWR | O_CREAT | O_TRUNC, 0666);=0A= =0A= if (fd !=3D -1)=0A= {=0A= if (write(fd, "0", 1) =3D=3D 1)=0A= {=0A= off_t pos =3D lseek(fd, 0, SEEK_CUR);=0A= =0A= if (pos !=3D (off_t)-1)=0A= {=0A= if (ftruncate(fd, 512) !=3D -1)=0A= {=0A= if (pos =3D=3D lseek(fd, 0, SEEK_CUR))=0A= {=0A= if (lseek(fd, 0, SEEK_SET) =3D=3D 0)=0A= {=0A= char buf[512];=0A= =0A= if (read(fd, buf, 512) =3D=3D 512)=0A= exitStatus =3D 0;=0A= }=0A= }=0A= }=0A= }=0A= }=0A= close(fd);=0A= unlink(path);=0A= }=0A= }=0A= =0A= return exitStatus;=0A= }=0A= =0A= configure:2952: checking for working alloca.h=0A= configure:2985: checking for alloca=0A= configure:3050: checking whether alloca needs Cray hooks=0A= configure:3135: checking stack direction for C alloca=0A= configure:3184: checking for st_blksize in struct stat=0A= configure:3219: checking for IEEE floating point format=0A= configure:3257: c89 -o conftest -O -DNDEBUG conftest.c 1>&5=0A= No such feature exists (-5,116)=0A= =0A= The MIPSpro C Compiler =0A= (license FEATURE string =3D cc) =0A= requires a license password. =0A= =0A= For license installation and trouble shooting =0A= information visit the web page: =0A= =0A= http://www.sgi.com/Support/Licensing/install_docs.html =0A= =0A= To obtain a Permanent license (proof of purchase=0A= required) or an Evaluation license please=0A= visit our license request web page: =0A= =0A= http://www.sgi.com/Products/license.html =0A= =0A= or send a blank email message to: =0A= =0A= license@sgi.com =0A= =0A= In North America, Silicon Graphics' customers may request =0A= Permanent licenses by sending a facsimile to: =0A= =0A= (650) 932-0537 =0A= =0A= or by calling our technical support hotline =0A= =0A= 1-800-800-4SGI =0A= =0A= If you are Outside of North America or you are not a Silicon =0A= Graphics support customer then contact your local support provider. =0A= =0A= cc-3450 fec: INTERNAL =0A= open_message_catalog: cannot open message catalog file=0A= =0A= =0A= 1 catastrophic error detected in the compilation of "conftest.c".=0A= Compilation aborted.=0A= configure: failed program was:=0A= #line 3224 "configure"=0A= #include "confdefs.h"=0A= #ifndef NO_FLOAT_H=0A= #include =0A= #endif=0A= =0A= #define EXIT_NOTIEEE 1=0A= #define EXIT_MAYBEIEEE 0=0A= =0A= int=0A= main()=0A= {=0A= #if defined(FLT_RADIX) && FLT_RADIX !=3D 2=0A= return EXIT_NOTIEEE;=0A= #elif defined(DBL_MAX_EXP) && DBL_MAX_EXP !=3D 1024=0A= return EXIT_NOTIEEE;=0A= #elif defined(DBL_MANT_DIG) && DBL_MANT_DIG !=3D 53=0A= return EXIT_NOTIEEE;=0A= #elif defined(FLT_MAX_EXP) && !(FLT_MAX_EXP =3D=3D 1024 || FLT_MAX_EXP = =3D=3D 128)=0A= return EXIT_NOTIEEE;=0A= #elif defined(FLT_MANT_DIG) && !(FLT_MANT_DIG =3D=3D 53 || FLT_MANT_DIG = =3D=3D 24)=0A= return EXIT_NOTIEEE;=0A= #else=0A= /* (assuming eight bit char) */=0A= if(sizeof(double) !=3D 8)=0A= return EXIT_NOTIEEE;=0A= if(!(sizeof(float) =3D=3D 4 || sizeof(float) =3D=3D 8))=0A= return EXIT_NOTIEEE;=0A= =0A= return EXIT_MAYBEIEEE;=0A= #endif=0A= }=0A= configure:3278: checking for ANSI C header files=0A= configure:3382: checking for size_t=0A= configure:3415: checking for off_t=0A= configure:3448: checking for ssize_t=0A= configure:3481: checking for ptrdiff_t=0A= configure:3514: checking for uchar=0A= configure:3547: checking whether char is unsigned=0A= configure:3610: checking whether byte ordering is bigendian=0A= configure:3700: checking size of short=0A= configure:3739: checking size of int=0A= configure:3778: checking size of long=0A= configure:3817: checking size of float=0A= configure:3856: checking size of double=0A= configure:3895: checking size of off_t=0A= configure:3938: checking size of size_t=0A= configure:4062: checking for manual-page index command=0A= configure:4066: checking binary distribution directory=0A= ------=_NextPart_000_0035_01C35D8B.22C9E580-- From minc-users@bic.mni.mcgill.ca Fri Aug 8 14:37:10 2003 From: minc-users@bic.mni.mcgill.ca (Jason Lerch) Date: Fri, 08 Aug 2003 09:37:10 -0400 Subject: [MINC-users] talairach volume and talairach center In-Reply-To: <1060291078.4670.13.camel@tosa-nb.nmr.mgh.harvard.edu> References: <1060291078.4670.13.camel@tosa-nb.nmr.mgh.harvard.edu> Message-ID: <1060349830.18989.2.camel@dennis.bic.mni.mcgill.ca> Greetings, the exact voxel coordinates are not going to tell you all that much about the accuracy of the talairach registration. Odds are that you are better off looking at the world 0,0,0 coordinates in some visualisation tool like register or Display. I think that you'll find us being quite close to the AC-PC line, though our registration procedure does not give any special meaning to that point, so it is possible for it to be off by a few millimetres even in a good registration. Cheers, Jason On Thu, 2003-08-07 at 17:17, Yasunari Tosa wrote: > Hi, MINC people > > I'm very confused about the talairach coordinate system > and I would appreciate it very much if you could clarify. > > My question: > Where is the talairach origin in the talairached volume? > > I thought that average_305.mnc is the one aligned with > talairach map (the web page says that it can be directly > superimposed over the talairach atlas). Thus I thought > that this is the "standard" talairached volume. > > When I did > > worldtovoxel average_305.mnc 0 0 0 > > returned non-trivial big values compared with the volume size. > > 68.25 126.51000000000000512 86.094999999999998863 > > Here is the MINC linear map stored > > MINC Linear Transform > 1.0000 0.0000 0.0000 -86.0950 > 0.0000 1.0000 0.0000 -126.5100 > 0.0000 0.0000 1.0000 -68.2500 > 0.0000 0.0000 0.0000 1.0000 > > This means that the average_305 volume center is not the > talairach origin. > > Is this a correct understanding? > > Thank you. > > Tosa > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From minc-users@bic.mni.mcgill.ca Fri Aug 8 14:40:06 2003 From: minc-users@bic.mni.mcgill.ca (Jason Lerch) Date: Fri, 08 Aug 2003 09:40:06 -0400 Subject: [MINC-users] talairach volume and talairach center In-Reply-To: <003801c35da4$48497820$d03384c8@PUCRS.BR> References: <1060291078.4670.13.camel@tosa-nb.nmr.mgh.harvard.edu> <003801c35da4$48497820$d03384c8@PUCRS.BR> Message-ID: <1060350006.18989.5.camel@dennis.bic.mni.mcgill.ca> Hello Mauricio, this appears to be much more of a problem with your MIPS PRO compilers than with our bits of software. See if you can get them reinstalled/upgraded; your other option is to get some version of gcc for IRIX - all of our bits of code can be compiled with gcc as well. Good luck, Jason On Fri, 2003-08-08 at 07:57, CDI HSL - Ressonancia wrote: > Hi everybody! > > I´ve been trying to install Display in a Irix 6.5.8 system but the necessary > libraries (netcdf, minc, opengl) are not possible to install because there > is a missing file called "fec" that should be in the directory > /usr/lib32/cmplrs. The configure log file is attatched, maybe it help you to > help me. > > Regards > > Mauricio > > > ----- Original Message ----- > From: Yasunari Tosa > To: > Sent: Thursday, August 07, 2003 6:17 PM > Subject: [MINC-users] talairach volume and talairach center > > > > Hi, MINC people > > > > I'm very confused about the talairach coordinate system > > and I would appreciate it very much if you could clarify. > > > > My question: > > Where is the talairach origin in the talairached volume? > > > > I thought that average_305.mnc is the one aligned with > > talairach map (the web page says that it can be directly > > superimposed over the talairach atlas). Thus I thought > > that this is the "standard" talairached volume. > > > > When I did > > > > worldtovoxel average_305.mnc 0 0 0 > > > > returned non-trivial big values compared with the volume size. > > > > 68.25 126.51000000000000512 86.094999999999998863 > > > > Here is the MINC linear map stored > > > > MINC Linear Transform > > 1.0000 0.0000 0.0000 -86.0950 > > 0.0000 1.0000 0.0000 -126.5100 > > 0.0000 0.0000 1.0000 -68.2500 > > 0.0000 0.0000 0.0000 1.0000 > > > > This means that the average_305 volume center is not the > > talairach origin. > > > > Is this a correct understanding? > > > > Thank you. > > > > Tosa > > > > > > _______________________________________________ > > MINC-users@bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From minc-users@bic.mni.mcgill.ca Tue Aug 12 23:31:13 2003 From: minc-users@bic.mni.mcgill.ca (Yasunari Tosa) Date: Tue, 12 Aug 2003 18:31:13 -0400 Subject: [MINC-users] autoreg result differences between 0.98i and 0.98j Message-ID: <1060727473.1827.51.camel@tosa-nb.nmr.mgh.harvard.edu> --=-9KEbeNWuoDIPDbWHgaLX Content-Type: text/plain Content-Transfer-Encoding: 7bit Hi, MINC people: I'm slightly perplexed about the result differences between autoreg 0.98i with MNI 1.0.4 and 0.98j with MNI 1.1. (I did "mritotal -protocol icbm long.mnc long.xfm"). Can you characterize the differences between two versions ? Here is the differences between two results and I see the translation of .3 mm differences. /home/tosa/dev/utils/test/longtest>cat long.xfm longold.xfm MNI Transform File %Tue Aug 12 17:51:30 2003>>> /usr/pubsw/packages/mni/1.1/bin/minctracc /tmp/mritotal_2564/long_8_dxyz.mnc /usr/pubsw/packages/mni/1.1/share/mni_autoreg/average_305_8_dxyz.mnc long.xfm -transformation /tmp/mritotal_2564/long_8tmp2c.xfm -lsq9 -xcorr -model_mask /usr/pubsw/packages/mni/1.1/share/mni_autoreg/average_305_8_mask.mnc -center 2.278679 17.403790 -21.946451 -step 4 4 4 -tol 0.004 -simplex 2 %(Package MNI AutoReg, version 0.98j, compiled by tosa@tosa-nb (i686-pc-linux-gnu) on 2003-08-06 at 11:36:23) Transform_Type = Linear; Linear_Transform = 1.06406915187836 0.0631770119071007 0.0751103684306145 -0.116913199424744 -0.08913454413414 1.06870532035828 0.363834142684937 -8.67768859863281 -0.0572138950228691 -0.393351554870605 1.14139127731323 4.30908584594727; MNI Transform File %Tue Aug 12 18:18:04 2003>>> /usr/pubsw/packages/mni/1.0.4/bin/minctracc /tmp/mritotal_2764/long_8_dxyz.mnc /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/average_305_8_dxyz.mnc longold.xfm -transformation /tmp/mritotal_2764/long_8tmp2c.xfm -lsq9 -xcorr -model_mask /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/average_305_8_mask.mnc -center 2.278679 17.403790 -21.946451 -step 4 4 4 -tol 0.004 -simplex 2 %(Package MNI AutoReg, version 0.98i, compiled by pubsw@lyon (i686-pc-linux-gnu) on 2001-08-09 at 10:20:06) Transform_Type = Linear; Linear_Transform = 1.06973445415497 0.0605374500155449 0.0805094987154007 -0.114964365959167 -0.0875343009829521 1.07748556137085 0.352880418300629 -8.94868469238281 -0.0643798187375069 -0.378622025251389 1.14011538028717 4.07937240600586; -- Yasunari Tosa, Ph.D. R&D Enginner email: tosa@nmr.mgh.harvard.edu Mass. General Hospital NMR Center phone: Building 149-2301 13th Street fax : Charlestown, MA 02129 --=-9KEbeNWuoDIPDbWHgaLX Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 7bit Hi, MINC people:

I'm slightly perplexed about the result differences between autoreg 0.98i with MNI 1.0.4 and 0.98j with MNI 1.1.
(I did "mritotal -protocol icbm long.mnc long.xfm").

Can you characterize the differences between two versions ?

Here is the differences between two results and I see the translation of .3 mm differences.

/home/tosa/dev/utils/test/longtest>cat long.xfm longold.xfm
MNI Transform File
%Tue Aug 12 17:51:30 2003>>> /usr/pubsw/packages/mni/1.1/bin/minctracc /tmp/mritotal_2564/long_8_dxyz.mnc /usr/pubsw/packages/mni/1.1/share/mni_autoreg/average_305_8_dxyz.mnc long.xfm -transformation /tmp/mritotal_2564/long_8tmp2c.xfm -lsq9 -xcorr -model_mask /usr/pubsw/packages/mni/1.1/share/mni_autoreg/average_305_8_mask.mnc -center 2.278679 17.403790 -21.946451 -step 4 4 4 -tol 0.004 -simplex 2
%(Package MNI AutoReg, version 0.98j, compiled by tosa@tosa-nb (i686-pc-linux-gnu) on 2003-08-06 at 11:36:23)

Transform_Type = Linear;
Linear_Transform =
1.06406915187836 0.0631770119071007 0.0751103684306145 -0.116913199424744
-0.08913454413414 1.06870532035828 0.363834142684937 -8.67768859863281
-0.0572138950228691 -0.393351554870605 1.14139127731323 4.30908584594727;
MNI Transform File
%Tue Aug 12 18:18:04 2003>>> /usr/pubsw/packages/mni/1.0.4/bin/minctracc /tmp/mritotal_2764/long_8_dxyz.mnc /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/average_305_8_dxyz.mnc longold.xfm -transformation /tmp/mritotal_2764/long_8tmp2c.xfm -lsq9 -xcorr -model_mask /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/average_305_8_mask.mnc -center 2.278679 17.403790 -21.946451 -step 4 4 4 -tol 0.004 -simplex 2
%(Package MNI AutoReg, version 0.98i, compiled by pubsw@lyon (i686-pc-linux-gnu) on 2001-08-09 at 10:20:06)

Transform_Type = Linear;
Linear_Transform =
1.06973445415497 0.0605374500155449 0.0805094987154007 -0.114964365959167
-0.0875343009829521 1.07748556137085 0.352880418300629 -8.94868469238281
-0.0643798187375069 -0.378622025251389 1.14011538028717 4.07937240600586;



-- 
Yasunari Tosa, Ph.D.
R&D Enginner				email: tosa@nmr.mgh.harvard.edu
Mass. General Hospital NMR Center	phone:  		
Building 149-2301
13th Street			        fax  :
Charlestown, MA 02129
--=-9KEbeNWuoDIPDbWHgaLX-- From minc-users@bic.mni.mcgill.ca Tue Aug 12 23:48:54 2003 From: minc-users@bic.mni.mcgill.ca (Steve ROBBINS) Date: Tue, 12 Aug 2003 18:48:54 -0400 Subject: [MINC-users] autoreg result differences between 0.98i and 0.98j In-Reply-To: <1060727473.1827.51.camel@tosa-nb.nmr.mgh.harvard.edu>; from tosa@nmr.mgh.harvard.edu on Tue, Aug 12, 2003 at 06:31:13PM -0400 References: <1060727473.1827.51.camel@tosa-nb.nmr.mgh.harvard.edu> Message-ID: <20030812184854.I2499100@shadow.bic.mni.mcgill.ca> On Tue, Aug 12, 2003 at 06:31:13PM -0400, Yasunari Tosa wrote: > Hi, MINC people: > > I'm slightly perplexed about the result differences between autoreg > 0.98i with MNI 1.0.4 and 0.98j with MNI 1.1. > (I did "mritotal -protocol icbm long.mnc long.xfm"). > > Can you characterize the differences between two versions ? I just checked CVS to be sure: the only difference between MNI autoreg 0.98i and 0.98j is the configure script. There were no changes to the code. -Steve From minc-users@bic.mni.mcgill.ca Wed Aug 13 17:55:49 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Wed, 13 Aug 2003 12:55:49 -0400 (EDT) Subject: [MINC-users] Problems to compile and install Register and Display Message-ID: Hi I am installing the Register and Display into my Linux RedHat 9, however, I had problems with these two packages. I installed netCDF, MincTools and BicPL without problems using the source code and compile them. It seems that is missing some graphics library, but I don't know which. Below is what I got when I run "configure": [root@localhost local]# cd Register-1.3.2 [root@localhost Register-1.3.2]# ./configure --prefix=/usr/local/mni --with-build-path=/usr/local/mni creating cache ./config.cache checking for a BSD compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for mawk... no checking for gawk... gawk checking whether make sets ${MAKE}... yes checking for gcc... /usr/bin/cc checking whether the C compiler (/usr/bin/cc -O ) works... yes checking whether the C compiler (/usr/bin/cc -O ) is a cross-compiler... no checking whether we are using GNU C... yes checking whether /usr/bin/cc accepts -g... yes checking for style of include used by make... GNU checking dependency style of /usr/bin/cc... gcc3 checking whether ln -s works... yes checking whether make sets ${MAKE}... (cached) yes checking for ranlib... ranlib checking how to run the C preprocessor... /usr/bin/cc -E checking for X... libraries /usr/X11R6/lib, headers /usr/X11R6/include checking for dnet_ntoa in -ldnet... no checking for dnet_ntoa in -ldnet_stub... no checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking for ANSI C header files... yes checking for sys/wait.h that is POSIX.1 compatible... yes checking for fcntl.h... yes checking for limits.h... yes checking for unistd.h... yes checking for math.h... yes checking for sqrt in -lm... yes checking for netcdf.h... yes checking for ncopen in -lnetcdf... yes checking for minc.h... yes checking for miicv_create in -lminc... yes checking for volume_io.h... yes checking for input_volume in -lvolume_io... yes checking for bicpl.h... yes checking for input_graphics_file in -lbicpl... yes checking for GL/gl.h... yes checking for glBegin in -lGL... yes checking for GL/glu.h... yes checking for gluLookAt in -lGLU... yes checking for GL/glut.h... yes checking for glutInit in -lglut... no configure: error: cannot find required library [root@localhost Register-1.3.2]# Thanks. -- Andre Matos amatos@mrs.mni.mcgill.ca From minc-users@bic.mni.mcgill.ca Wed Aug 13 18:54:17 2003 From: minc-users@bic.mni.mcgill.ca (Steve ROBBINS) Date: Wed, 13 Aug 2003 13:54:17 -0400 Subject: [MINC-users] Problems to compile and install Register and Display In-Reply-To: ; from amatos@mrs.mni.mcgill.ca on Wed, Aug 13, 2003 at 12:55:49PM -0400 References: Message-ID: <20030813135417.A5323@shadow.bic.mni.mcgill.ca> On Wed, Aug 13, 2003 at 12:55:49PM -0400, Andre MATOS wrote: > Hi > > I am installing the Register and Display into my Linux RedHat 9, however, > I had problems with these two packages. I installed netCDF, MincTools and > BicPL without problems using the source code and compile them. > > It seems that is missing some graphics library, but I don't know which. [...] > checking for glutInit in -lglut... no > configure: error: cannot find required library It's libglut that is missing. You'll need the "development" package from redhat. Regards, -Steve From minc-users@bic.mni.mcgill.ca Wed Aug 13 18:59:10 2003 From: minc-users@bic.mni.mcgill.ca (Jason Lerch) Date: Wed, 13 Aug 2003 13:59:10 -0400 Subject: [MINC-users] Problems to compile and install Register and Display In-Reply-To: References: Message-ID: <1060797550.5763.13.camel@dennis.bic.mni.mcgill.ca> Hello, GLUT is missing. Make sure it is installed; install it if not. If it is installed, make sure that libglut.a or libglut.so is somewhere on your search path or set the environment variable LD_LIBRARY_PATH to reflect its location before running configure. Cheers, Jason On Wed, 2003-08-13 at 12:55, Andre MATOS wrote: > Hi > > I am installing the Register and Display into my Linux RedHat 9, however, > I had problems with these two packages. I installed netCDF, MincTools and > BicPL without problems using the source code and compile them. > > It seems that is missing some graphics library, but I don't know which. > > Below is what I got when I run "configure": > > > [root@localhost local]# cd Register-1.3.2 > [root@localhost Register-1.3.2]# ./configure --prefix=/usr/local/mni > --with-build-path=/usr/local/mni > creating cache ./config.cache > checking for a BSD compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > checking for mawk... no > checking for gawk... gawk > checking whether make sets ${MAKE}... yes > checking for gcc... /usr/bin/cc > checking whether the C compiler (/usr/bin/cc -O ) works... yes > checking whether the C compiler (/usr/bin/cc -O ) is a cross-compiler... > no > checking whether we are using GNU C... yes > checking whether /usr/bin/cc accepts -g... yes > checking for style of include used by make... GNU > checking dependency style of /usr/bin/cc... gcc3 > checking whether ln -s works... yes > checking whether make sets ${MAKE}... (cached) yes > checking for ranlib... ranlib > checking how to run the C preprocessor... /usr/bin/cc -E > checking for X... libraries /usr/X11R6/lib, headers /usr/X11R6/include > checking for dnet_ntoa in -ldnet... no > checking for dnet_ntoa in -ldnet_stub... no > checking for gethostbyname... yes > checking for connect... yes > checking for remove... yes > checking for shmat... yes > checking for IceConnectionNumber in -lICE... yes > checking for ANSI C header files... yes > checking for sys/wait.h that is POSIX.1 compatible... yes > checking for fcntl.h... yes > checking for limits.h... yes > checking for unistd.h... yes > checking for math.h... yes > checking for sqrt in -lm... yes > checking for netcdf.h... yes > checking for ncopen in -lnetcdf... yes > checking for minc.h... yes > checking for miicv_create in -lminc... yes > checking for volume_io.h... yes > checking for input_volume in -lvolume_io... yes > checking for bicpl.h... yes > checking for input_graphics_file in -lbicpl... yes > checking for GL/gl.h... yes > checking for glBegin in -lGL... yes > checking for GL/glu.h... yes > checking for gluLookAt in -lGLU... yes > checking for GL/glut.h... yes > checking for glutInit in -lglut... no > configure: error: cannot find required library > [root@localhost Register-1.3.2]# > > > > > > Thanks. From minc-users@bic.mni.mcgill.ca Thu Aug 14 03:04:15 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Wed, 13 Aug 2003 22:04:15 -0400 (EDT) Subject: [MINC-users] Problems to compile and install Register and Display In-Reply-To: <1060797550.5763.13.camel@dennis.bic.mni.mcgill.ca> Message-ID: Hy Jason, I think it is installed because I found the libglut.so into directory /usr/lib I tried to set LD_LIBRARY_PATH to this directory and also include it into my PATH, however I am still getting the same error. What do you think? Thanks, Andre Matos amatos@mrs.mni.mcgill.ca On Wed, 13 Aug 2003, Jason Lerch wrote: > Hello, > > GLUT is missing. Make sure it is installed; install it if not. If it is > installed, make sure that libglut.a or libglut.so is somewhere on your > search path or set the environment variable LD_LIBRARY_PATH to reflect > its location before running configure. > > Cheers, > > Jason > > On Wed, 2003-08-13 at 12:55, Andre MATOS wrote: > > Hi > > > > I am installing the Register and Display into my Linux RedHat 9, however, > > I had problems with these two packages. I installed netCDF, MincTools and > > BicPL without problems using the source code and compile them. > > > > It seems that is missing some graphics library, but I don't know which. > > > > Below is what I got when I run "configure": > > > > > > [root@localhost local]# cd Register-1.3.2 > > [root@localhost Register-1.3.2]# ./configure --prefix=/usr/local/mni > > --with-build-path=/usr/local/mni > > creating cache ./config.cache > > checking for a BSD compatible install... /usr/bin/install -c > > checking whether build environment is sane... yes > > checking for mawk... no > > checking for gawk... gawk > > checking whether make sets ${MAKE}... yes > > checking for gcc... /usr/bin/cc > > checking whether the C compiler (/usr/bin/cc -O ) works... yes > > checking whether the C compiler (/usr/bin/cc -O ) is a cross-compiler... > > no > > checking whether we are using GNU C... yes > > checking whether /usr/bin/cc accepts -g... yes > > checking for style of include used by make... GNU > > checking dependency style of /usr/bin/cc... gcc3 > > checking whether ln -s works... yes > > checking whether make sets ${MAKE}... (cached) yes > > checking for ranlib... ranlib > > checking how to run the C preprocessor... /usr/bin/cc -E > > checking for X... libraries /usr/X11R6/lib, headers /usr/X11R6/include > > checking for dnet_ntoa in -ldnet... no > > checking for dnet_ntoa in -ldnet_stub... no > > checking for gethostbyname... yes > > checking for connect... yes > > checking for remove... yes > > checking for shmat... yes > > checking for IceConnectionNumber in -lICE... yes > > checking for ANSI C header files... yes > > checking for sys/wait.h that is POSIX.1 compatible... yes > > checking for fcntl.h... yes > > checking for limits.h... yes > > checking for unistd.h... yes > > checking for math.h... yes > > checking for sqrt in -lm... yes > > checking for netcdf.h... yes > > checking for ncopen in -lnetcdf... yes > > checking for minc.h... yes > > checking for miicv_create in -lminc... yes > > checking for volume_io.h... yes > > checking for input_volume in -lvolume_io... yes > > checking for bicpl.h... yes > > checking for input_graphics_file in -lbicpl... yes > > checking for GL/gl.h... yes > > checking for glBegin in -lGL... yes > > checking for GL/glu.h... yes > > checking for gluLookAt in -lGLU... yes > > checking for GL/glut.h... yes > > checking for glutInit in -lglut... no > > configure: error: cannot find required library > > [root@localhost Register-1.3.2]# > > > > > > > > > > > > Thanks. > > _______________________________________________ > 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 Thu Aug 14 03:10:20 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Wed, 13 Aug 2003 22:10:20 -0400 (EDT) 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, Is this "development" package the same that we can choose when we select the packages that we want to install at the installation time? If is yes, I selected and I have installed the X Window System, Development Tools, Kernel Development, X Software Development, GNOME Software Development and KDE Software Developement. All these I selected all packages. If is not this, what is it and where I can get it. Thanks. Andre Matos amatos@mrs.mni.mcgill.ca On Wed, 13 Aug 2003, Steve ROBBINS wrote: > On Wed, Aug 13, 2003 at 12:55:49PM -0400, Andre MATOS wrote: > > Hi > > > > I am installing the Register and Display into my Linux RedHat 9, however, > > I had problems with these two packages. I installed netCDF, MincTools and > > BicPL without problems using the source code and compile them. > > > > It seems that is missing some graphics library, but I don't know which. > > [...] > > > checking for glutInit in -lglut... no > > configure: error: cannot find required library > > It's libglut that is missing. You'll need the "development" package from > redhat. > > 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 Thu Aug 14 03:24:08 2003 From: minc-users@bic.mni.mcgill.ca (Steve ROBBINS) Date: Wed, 13 Aug 2003 22:24:08 -0400 Subject: [MINC-users] Problems to compile and install Register and Display In-Reply-To: ; from amatos@mrs.mni.mcgill.ca on Wed, Aug 13, 2003 at 10:04:15PM -0400 References: <20030813135417.A5323@shadow.bic.mni.mcgill.ca> <1060797550.5763.13.camel@dennis.bic.mni.mcgill.ca> Message-ID: <20030813222408.C5323@shadow.bic.mni.mcgill.ca> On Wed, Aug 13, 2003 at 10:04:15PM -0400, Andre MATOS wrote: > Hy Jason, > > I think it is installed because I found the libglut.so into directory > /usr/lib That suggests you have the development package installed. In the directory in which you run "configure", you will find a file named "config.log". Have a look in there for the error messages related to glut. If they don't point to anything helpful, send me the config.log file in private email (it's pretty big). > I tried to set LD_LIBRARY_PATH to this directory and also include it into > my PATH, however I am still getting the same error. Don't set the PATH nor LD_LIBRARY_PATH. -S