From jween at klaru-baycrest.on.ca Wed Mar 4 21:40:47 2009 From: jween at klaru-baycrest.on.ca (Jon Erik Ween) Date: Wed, 4 Mar 2009 21:40:47 -0500 Subject: [MINC-users] dyld errors In-Reply-To: References: Message-ID: <3865382F-FC0F-4A30-B8EE-EA92F4B8B713@klaru-baycrest.on.ca> Friends (and the rest) Well, I've been able to compile and install most of the tools (OS X 10.5.6 MacPro) and they seem to work, except: 1) Can't build any of the visualizers (Display, register, etc) due to OpenGL linking problems and Netpbm problems (even having installed fink, sourced /sw/bin/init.sh, etc.) The error I get using pre- compiled versions of Display now is: dyld: Library not loaded: /libnetpbm.10.dylib Referenced from: /usr/local/mni2/bin/Display Reason: no suitable image found. Did find: /sw/lib//libnetpbm.10.dylib: mach-o, but wrong architecture 2) Can't get Alex's 64 bit package to run (with the libs in that package or /sw/lib). Error: bash-3.2$ ./Display dyld: Symbol not found: __cg_jpeg_resync_to_restart Referenced from: /System/Library/Frameworks/ ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ Versions/A/ImageIO Expected in: /Users/jween/Desktop/bic_tools/lib/libJPEG.dylib I guess I'm ignorant about how to get the dynamic libraries to link properly, or what links exist are pointing in the wrong direction. Tried to comile netpbm from scratch, but couldn't find the jpg and tiff libs, etc. Any hints would be appreciated. Thanks Jon Soli Deo Gloria Jon Erik Ween, MD, MS Scientist, Kunin-Lunenfeld Applied Research Unit Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre Assistant Professor, Dept. of Medicine, Div. of Neurology University of Toronto Faculty of Medicine Kimel Family Building, 6th Floor, Room 644 Baycrest Centre 3560 Bathurst Street Toronto, Ontario M6A 2E1 Canada Phone: 416-785-2500 x3648 Fax: 416-785-2484 Email: jween at klaru-baycrest.on.ca Confidential: This communication and any attachment(s) may contain confidential or privileged information and is intended solely for the address(es) or the entity representing the recipient(s). If you have received this information in error, you are hereby advised to destroy the document and any attachment(s), make no copies of same and inform the sender immediately of the error. Any unauthorized use or disclosure of this information is strictly prohibited. On 11-Feb-09, at 8:21 PM, Andrew Janke wrote: > Hi Jon, > > 2009/2/12 Jon Erik Ween : >> Friends > > Romans... ? > >> I just migrated from Linux to OS X 10.5, but can't figure out how to >> set the dynamic linker variables correctly to link to libs in /usr/ >> local and so forth. > > Hrm. Have you got the fink'ish stuff in your .bashrc? > > . /sw/bin/init.sh > > > -- > Andrew Janke > (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canberra->Australia +61 (402) 700 883 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From sandeepdhankhar at gmail.com Wed Mar 4 21:48:51 2009 From: sandeepdhankhar at gmail.com (sandeep dhankhar) Date: Wed, 4 Mar 2009 20:48:51 -0600 Subject: [MINC-users] dyld errors In-Reply-To: <3865382F-FC0F-4A30-B8EE-EA92F4B8B713@klaru-baycrest.on.ca> References: <3865382F-FC0F-4A30-B8EE-EA92F4B8B713@klaru-baycrest.on.ca> Message-ID: <826ac67c0903041848u3f9a96fch367984186283308b@mail.gmail.com> Hi, I also faced problems regarding libraries for openGL in mac. It sounds strange but I counld not help it for one week , later on I tried using the frameworks provided in mac for openGL and that works fine for me now.I am not sure if it helps you. Sandeep On Wed, Mar 4, 2009 at 8:40 PM, Jon Erik Ween wrote: > Friends (and the rest) > > Well, I've been able to compile and install most of the tools (OS X > 10.5.6 MacPro) and they seem to work, except: > > 1) Can't build any of the visualizers (Display, register, etc) due to > OpenGL linking problems and Netpbm problems (even having installed > fink, sourced /sw/bin/init.sh, etc.) The error I get using pre- > compiled versions of Display now is: > > dyld: Library not loaded: /libnetpbm.10.dylib > Referenced from: /usr/local/mni2/bin/Display > Reason: no suitable image found. Did find: > /sw/lib//libnetpbm.10.dylib: mach-o, but wrong architecture > > 2) Can't get Alex's 64 bit package to run (with the libs in that > package or /sw/lib). Error: > > bash-3.2$ ./Display > dyld: Symbol not found: __cg_jpeg_resync_to_restart > Referenced from: /System/Library/Frameworks/ > ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ > Versions/A/ImageIO > Expected in: /Users/jween/Desktop/bic_tools/lib/libJPEG.dylib > > I guess I'm ignorant about how to get the dynamic libraries to link > properly, or what links exist are pointing in the wrong direction. > Tried to comile netpbm from scratch, but couldn't find the jpg and > tiff libs, etc. > > Any hints would be appreciated. > > Thanks > > Jon > > Soli Deo Gloria > > Jon Erik Ween, MD, MS > Scientist, Kunin-Lunenfeld Applied Research Unit > Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre > Assistant Professor, Dept. of Medicine, Div. of Neurology > University of Toronto Faculty of Medicine > > Kimel Family Building, 6th Floor, Room 644 > Baycrest Centre > 3560 Bathurst Street > Toronto, Ontario M6A 2E1 > Canada > > Phone: 416-785-2500 x3648 > Fax: 416-785-2484 > Email: jween at klaru-baycrest.on.ca > > > Confidential: This communication and any attachment(s) may contain > confidential or privileged information and is intended solely for the > address(es) or the entity representing the recipient(s). If you have > received this information in error, you are hereby advised to destroy > the document and any attachment(s), make no copies of same and inform > the sender immediately of the error. Any unauthorized use or > disclosure of this information is strictly prohibited. > > > > On 11-Feb-09, at 8:21 PM, Andrew Janke wrote: > > > Hi Jon, > > > > 2009/2/12 Jon Erik Ween : > >> Friends > > > > Romans... ? > > > >> I just migrated from Linux to OS X 10.5, but can't figure out how to > >> set the dynamic linker variables correctly to link to libs in /usr/ > >> local and so forth. > > > > Hrm. Have you got the fink'ish stuff in your .bashrc? > > > > . /sw/bin/init.sh > > > > > > -- > > Andrew Janke > > (a.janke at gmail.com || http://a.janke.googlepages.com/) > > Canberra->Australia +61 (402) 700 883 > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Fri Mar 6 06:25:43 2009 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 6 Mar 2009 22:25:43 +1100 Subject: [MINC-users] dyld errors In-Reply-To: <3865382F-FC0F-4A30-B8EE-EA92F4B8B713@klaru-baycrest.on.ca> References: <3865382F-FC0F-4A30-B8EE-EA92F4B8B713@klaru-baycrest.on.ca> Message-ID: Hi Jon, Looks a tad ugly (and suspiciously like Apple have fiddled with a few things... Especially the wrong architecture bit). The only 10.5 machine at my disposal reports this: rotor$ uname -a Darwin 9.4.0 Darwin Kernel Version 9.4.0: Mon Jun 9 19:30:53 PDT 2008; root:xnu-1228.5.20~1/RELEASE_I386 i386 rotor$ sw_vers ProductName: Mac OS X ProductVersion: 10.5.4 BuildVersion: 9E17 I'll be interested to know what yours reports. -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 On Thu, Mar 5, 2009 at 13:40, Jon Erik Ween wrote: > Friends (and the rest) > > Well, I've been able to compile and install most of the tools (OS X > 10.5.6 MacPro) and they seem to work, except: > > 1) Can't build any of the visualizers (Display, register, etc) due to > OpenGL linking problems and Netpbm problems (even having installed > fink, sourced /sw/bin/init.sh, ?etc.) The error I get using pre- > compiled versions of Display now is: > > dyld: Library not loaded: /libnetpbm.10.dylib > ? Referenced from: /usr/local/mni2/bin/Display > ? Reason: no suitable image found. ?Did find: > ? ? ? ? /sw/lib//libnetpbm.10.dylib: mach-o, but wrong architecture > > 2) Can't get Alex's 64 bit package to run (with the libs in that > package or /sw/lib). Error: > > bash-3.2$ ./Display > dyld: Symbol not found: __cg_jpeg_resync_to_restart > ? Referenced from: /System/Library/Frameworks/ > ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ > Versions/A/ImageIO > ? Expected in: /Users/jween/Desktop/bic_tools/lib/libJPEG.dylib > > I guess I'm ignorant about how to get the dynamic libraries to link > properly, or what links exist are pointing in the wrong direction. > Tried to comile netpbm from scratch, but couldn't find the jpg and > tiff libs, etc. > > Any hints would be appreciated. > > Thanks > > Jon > > Soli Deo Gloria > > Jon Erik Ween, MD, MS > Scientist, Kunin-Lunenfeld Applied Research Unit > Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre > Assistant Professor, Dept. of Medicine, Div. of Neurology > ? ? University of Toronto Faculty of Medicine > > Kimel Family Building, 6th Floor, Room 644 > Baycrest Centre > 3560 Bathurst Street > Toronto, Ontario M6A 2E1 > Canada > > Phone: 416-785-2500 x3648 > Fax: 416-785-2484 > Email: jween at klaru-baycrest.on.ca > > > Confidential: This communication and any attachment(s) may contain > confidential or privileged information and is intended solely for the > address(es) or the entity representing the recipient(s). If you have > received this information in error, you are hereby advised to destroy > the document and any attachment(s), make no copies of same and inform > the sender immediately of the error. Any unauthorized use or > disclosure of this information is strictly prohibited. > > > > On 11-Feb-09, at 8:21 PM, Andrew Janke wrote: > >> Hi Jon, >> >> 2009/2/12 Jon Erik Ween : >>> Friends >> >> Romans... ? >> >>> I just migrated from Linux to OS X 10.5, but can't figure out how to >>> set the dynamic linker variables correctly to link to libs in /usr/ >>> local and so forth. >> >> Hrm. ?Have you got the fink'ish stuff in your .bashrc? >> >> ? . /sw/bin/init.sh >> >> >> -- >> Andrew Janke >> (a.janke at gmail.com || http://a.janke.googlepages.com/) >> Canberra->Australia ? ?+61 (402) 700 883 >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From jween at klaru-baycrest.on.ca Fri Mar 6 07:21:29 2009 From: jween at klaru-baycrest.on.ca (Jon Erik Ween) Date: Fri, 6 Mar 2009 07:21:29 -0500 Subject: [MINC-users] dyld errors In-Reply-To: References: <3865382F-FC0F-4A30-B8EE-EA92F4B8B713@klaru-baycrest.on.ca> Message-ID: <332E7CF0-5D60-45AB-B011-C562F0E32DFF@klaru-baycrest.on.ca> Andrew Similar to yours: jween:~ jween$ uname -a Darwin jween.local 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386 jween:~ jween$ sw_vers ProductName: Mac OS X ProductVersion: 10.5.6 BuildVersion: 9G55 I find it a bit odd, but have not seen anywhere in my browsing how to change these settings to indicate that your native architecture is x86_64 but i'm betting it has an impact when you just naively compile things and don't deliberately set parameters to "cross-platform" compile. Jon Soli Deo Gloria On 6-Mar-09, at 6:25 AM, Andrew Janke wrote: > Hi Jon, > > Looks a tad ugly (and suspiciously like Apple have fiddled with a few > things... Especially the wrong architecture bit). The only 10.5 > machine at my disposal reports this: > > rotor$ uname -a > Darwin 9.4.0 Darwin Kernel Version 9.4.0: Mon Jun 9 19:30:53 PDT > 2008; root:xnu-1228.5.20~1/RELEASE_I386 i386 > > rotor$ sw_vers > ProductName: Mac OS X > ProductVersion: 10.5.4 > BuildVersion: 9E17 > > I'll be interested to know what yours reports. > > > -- > Andrew Janke > (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canberra->Australia +61 (402) 700 883 > > > On Thu, Mar 5, 2009 at 13:40, Jon Erik Ween > wrote: >> Friends (and the rest) >> >> Well, I've been able to compile and install most of the tools (OS X >> 10.5.6 MacPro) and they seem to work, except: >> >> 1) Can't build any of the visualizers (Display, register, etc) due to >> OpenGL linking problems and Netpbm problems (even having installed >> fink, sourced /sw/bin/init.sh, etc.) The error I get using pre- >> compiled versions of Display now is: >> >> dyld: Library not loaded: /libnetpbm.10.dylib >> Referenced from: /usr/local/mni2/bin/Display >> Reason: no suitable image found. Did find: >> /sw/lib//libnetpbm.10.dylib: mach-o, but wrong architecture >> >> 2) Can't get Alex's 64 bit package to run (with the libs in that >> package or /sw/lib). Error: >> >> bash-3.2$ ./Display >> dyld: Symbol not found: __cg_jpeg_resync_to_restart >> Referenced from: /System/Library/Frameworks/ >> ApplicationServices.framework/Versions/A/Frameworks/ >> ImageIO.framework/ >> Versions/A/ImageIO >> Expected in: /Users/jween/Desktop/bic_tools/lib/libJPEG.dylib >> >> I guess I'm ignorant about how to get the dynamic libraries to link >> properly, or what links exist are pointing in the wrong direction. >> Tried to comile netpbm from scratch, but couldn't find the jpg and >> tiff libs, etc. >> >> Any hints would be appreciated. >> >> Thanks >> >> Jon >> >> Soli Deo Gloria >> >> Jon Erik Ween, MD, MS >> Scientist, Kunin-Lunenfeld Applied Research Unit >> Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre >> Assistant Professor, Dept. of Medicine, Div. of Neurology >> University of Toronto Faculty of Medicine >> >> Kimel Family Building, 6th Floor, Room 644 >> Baycrest Centre >> 3560 Bathurst Street >> Toronto, Ontario M6A 2E1 >> Canada >> >> Phone: 416-785-2500 x3648 >> Fax: 416-785-2484 >> Email: jween at klaru-baycrest.on.ca >> >> >> Confidential: This communication and any attachment(s) may contain >> confidential or privileged information and is intended solely for the >> address(es) or the entity representing the recipient(s). If you have >> received this information in error, you are hereby advised to destroy >> the document and any attachment(s), make no copies of same and inform >> the sender immediately of the error. Any unauthorized use or >> disclosure of this information is strictly prohibited. >> >> >> >> On 11-Feb-09, at 8:21 PM, Andrew Janke wrote: >> >>> Hi Jon, >>> >>> 2009/2/12 Jon Erik Ween : >>>> Friends >>> >>> Romans... ? >>> >>>> I just migrated from Linux to OS X 10.5, but can't figure out how >>>> to >>>> set the dynamic linker variables correctly to link to libs in /usr/ >>>> local and so forth. >>> >>> Hrm. Have you got the fink'ish stuff in your .bashrc? >>> >>> . /sw/bin/init.sh >>> >>> >>> -- >>> Andrew Janke >>> (a.janke at gmail.com || http://a.janke.googlepages.com/) >>> Canberra->Australia +61 (402) 700 883 >>> _______________________________________________ >>> MINC-users at bic.mni.mcgill.ca >>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>> >> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From r.hoge at umontreal.ca Fri Mar 6 08:54:00 2009 From: r.hoge at umontreal.ca (Rick Hoge) Date: Fri, 6 Mar 2009 08:54:00 -0500 Subject: [MINC-users] dyld errors In-Reply-To: <332E7CF0-5D60-45AB-B011-C562F0E32DFF@klaru-baycrest.on.ca> References: <3865382F-FC0F-4A30-B8EE-EA92F4B8B713@klaru-baycrest.on.ca> <332E7CF0-5D60-45AB-B011-C562F0E32DFF@klaru-baycrest.on.ca> Message-ID: <4BC332FD-0484-4A88-A71C-414F1161E00D@umontreal.ca> Hi guys, Some info on Mac architectures: Apple hasn't sold a 32-bit processor in quite a while now - if you are running a recent (since late 2007) Mac Pro, MacBook, MacBook Pro, iMac, Mac Mini or whatever it will be a 64-bit processor (the only 32- bit Mac processor shipping now is the ARM in the iPhone). If "About this Mac" says you have a Core 2 Duo, it is 64-bit processor (Note that if it just says 'Core Duo' it's 32-bit). Build a "Hello World" program for x86_64 on a low-end MacBook and it will happily report that sizeof(void*) is 8, even though file / mach_kernel says /mach_kernel: Mach-O universal binary with 2 architectures /mach_kernel (for architecture i386): Mach-O executable i386 /mach_kernel (for architecture ppc): Mach-O executable ppc and uname -a gives Darwin Rick-MBP.local 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386 Confusion often arises from the fact that, in MacOSX 10.5, the *kernel* is the 32-bit i386 architecture, but it will happily run both i386 and x86_64 binaries (and ppc binaries for that matter, via Rosetta). The kernel does *not* need to be 64-bit for x86_64 apps to run. The inverse is not true - you can't run an x86_64 executable on a 32-bit "Core Duo" processor (the first Intel MacBooks). Recent 10.6 seeds have the 64-bit kernel enabled for some configurations (most systems that have shipped since early 2008). Rosetta will also probably be optional under 10.6 (which may or may not drop PPC support). In the Mac software world, you just build a 4-way fat binary (packaged with lipo) and the 'most natural' architecture is loaded at launch time. For cross-platform Unix software, the safest and easiest thing is often to build for a single arch but obviously you need to make sure that all libraries linked provide that architecture. Hope this helps - uname is not always a reliable way to get the full details on the architecture (in this case it happens to give the lowest common denominator that will run natively on the system). For some more information, see http://developer.apple.com/DOCUMENTATION/Darwin/Conceptual/64bitPorting/indications/chapter_2_section_2.html#/ /apple_ref/doc/uid/TP40001064-CH206-DontLinkElementID_21 The only thing that's missing is an answer to the question "how can I tell if my processor is 64-bit". I can't find any command-line utility (uname, arch, machine, etc.) that will generate an x86_64 output on my MacBook Pro (on which I'm developing and running all kinds of 64-bit stuff). Cheers, Rick > jween:~ jween$ uname -a > Darwin jween.local 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24 > 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386 > jween:~ jween$ sw_vers > ProductName: Mac OS X > ProductVersion: 10.5.6 > BuildVersion: 9G55 > > I find it a bit odd, but have not seen anywhere in my browsing how to > change these settings to indicate that your native architecture is > x86_64 but i'm betting it has an impact when you just naively compile > things and don't deliberately set parameters to "cross-platform" > compile. From r.hoge at umontreal.ca Fri Mar 6 09:39:37 2009 From: r.hoge at umontreal.ca (Rick Hoge) Date: Fri, 6 Mar 2009 09:39:37 -0500 Subject: [MINC-users] dyld errors In-Reply-To: <4BC332FD-0484-4A88-A71C-414F1161E00D@umontreal.ca> References: <3865382F-FC0F-4A30-B8EE-EA92F4B8B713@klaru-baycrest.on.ca> <332E7CF0-5D60-45AB-B011-C562F0E32DFF@klaru-baycrest.on.ca> <4BC332FD-0484-4A88-A71C-414F1161E00D@umontreal.ca> Message-ID: <830390A6-E4E5-4B54-BBD0-A5E20A313C42@umontreal.ca> Maybe this is more for the developer's list, but to follow up... > The only thing that's missing is an answer to the question "how can I > tell if my processor is 64-bit". I can't find any command-line > utility (uname, arch, machine, etc.) that will generate an x86_64 > output on my MacBook Pro (on which I'm developing and running all > kinds of 64-bit stuff). You *can* get the manufacturer's processor name on the command-line on a Mac using Rick-MBP:~ -> system_profiler | grep 'Processor Name' Processor Name: Intel Core 2 Duo But this does not explicitly indicate the pointer width. More painfully, you could build a tiny program that prints the value of sizeof(void*): echo "#include " > test.c echo "int main(int argc, char *argv[]) { fprintf(stdout,\"%d\n \",sizeof(void*)); return 0; }" >> test.c gcc -o test-64 -arch x86_64 test.c gcc -o test-32 -arch i386 test.c lipo -create test-64 test-32 -output test-fat running the 'test-fat' executable will print 4 on a 32-bit system, and 8 on a 64-bit system (prints 8 on my Core 2 Duo MacBook Pro). The new version of NeuroLens (to be released 'soon') indicates the architecture in the About panel using something like this. Rick From acveilleux at mrs.mni.mcgill.ca Fri Mar 6 12:19:27 2009 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Fri, 6 Mar 2009 12:19:27 -0500 Subject: [MINC-users] dyld errors In-Reply-To: <332E7CF0-5D60-45AB-B011-C562F0E32DFF@klaru-baycrest.on.ca>; from jween@klaru-baycrest.on.ca on Fri, Mar 06, 2009 at 07:21:29AM -0500 References: <3865382F-FC0F-4A30-B8EE-EA92F4B8B713@klaru-baycrest.on.ca> <332E7CF0-5D60-45AB-B011-C562F0E32DFF@klaru-baycrest.on.ca> Message-ID: <20090306121927.H2730@mrs.mni.mcgill.ca> Hi there, Assuming that you have Core 2 Duo or a Mac Pro, my "package" will normally run, if: 1) It's installed in /usr/local (the libs are expected to be in /usr/local/lib) 2) Clear DYLD_LIBRARY_PATH (Fink sets it and the linker gets hopelessly confused because of the f****** case-insensitive file-system). csh: setenv DYLD_LIBRARY_PATH "" ./Display bash: DYLD_LIBRARY_PATH="" ./Display I've been toying with rebuilding everything in 32-bit universal binaries for broader compatibility (and I have a Core Duo mac at home) but the time required is a bit daunting (the 32-bit build is much easier to do, but with my lab Mac Pro make -j8 makes up for that). Alex On Fri, Mar 06, 2009 at 07:21:29AM -0500, Jon Erik Ween wrote: > From: Jon Erik Ween > To: MINC users mailing list > Date: Fri, 6 Mar 2009 07:21:29 -0500 > X-Mailer: Apple Mail (2.930.3) > Subject: Re: [MINC-users] dyld errors > > Andrew > > Similar to yours: > > jween:~ jween$ uname -a > Darwin jween.local 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24 > 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386 > jween:~ jween$ sw_vers > ProductName: Mac OS X > ProductVersion: 10.5.6 > BuildVersion: 9G55 > > I find it a bit odd, but have not seen anywhere in my browsing how to > change these settings to indicate that your native architecture is > x86_64 but i'm betting it has an impact when you just naively compile > things and don't deliberately set parameters to "cross-platform" > compile. > > > > Jon > > Soli Deo Gloria > > > On 6-Mar-09, at 6:25 AM, Andrew Janke wrote: > > > Hi Jon, > > > > Looks a tad ugly (and suspiciously like Apple have fiddled with a few > > things... Especially the wrong architecture bit). The only 10.5 > > machine at my disposal reports this: > > > > rotor$ uname -a > > Darwin 9.4.0 Darwin Kernel Version 9.4.0: Mon Jun 9 19:30:53 PDT > > 2008; root:xnu-1228.5.20~1/RELEASE_I386 i386 > > > > rotor$ sw_vers > > ProductName: Mac OS X > > ProductVersion: 10.5.4 > > BuildVersion: 9E17 > > > > I'll be interested to know what yours reports. > > > > > > -- > > Andrew Janke > > (a.janke at gmail.com || http://a.janke.googlepages.com/) > > Canberra->Australia +61 (402) 700 883 > > > > > > On Thu, Mar 5, 2009 at 13:40, Jon Erik Ween > > wrote: > >> Friends (and the rest) > >> > >> Well, I've been able to compile and install most of the tools (OS X > >> 10.5.6 MacPro) and they seem to work, except: > >> > >> 1) Can't build any of the visualizers (Display, register, etc) due to > >> OpenGL linking problems and Netpbm problems (even having installed > >> fink, sourced /sw/bin/init.sh, etc.) The error I get using pre- > >> compiled versions of Display now is: > >> > >> dyld: Library not loaded: /libnetpbm.10.dylib > >> Referenced from: /usr/local/mni2/bin/Display > >> Reason: no suitable image found. Did find: > >> /sw/lib//libnetpbm.10.dylib: mach-o, but wrong architecture > >> > >> 2) Can't get Alex's 64 bit package to run (with the libs in that > >> package or /sw/lib). Error: > >> > >> bash-3.2$ ./Display > >> dyld: Symbol not found: __cg_jpeg_resync_to_restart > >> Referenced from: /System/Library/Frameworks/ > >> ApplicationServices.framework/Versions/A/Frameworks/ > >> ImageIO.framework/ > >> Versions/A/ImageIO > >> Expected in: /Users/jween/Desktop/bic_tools/lib/libJPEG.dylib > >> > >> I guess I'm ignorant about how to get the dynamic libraries to link > >> properly, or what links exist are pointing in the wrong direction. > >> Tried to comile netpbm from scratch, but couldn't find the jpg and > >> tiff libs, etc. > >> > >> Any hints would be appreciated. > >> > >> Thanks > >> > >> Jon > >> > >> Soli Deo Gloria > >> > >> Jon Erik Ween, MD, MS > >> Scientist, Kunin-Lunenfeld Applied Research Unit > >> Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre > >> Assistant Professor, Dept. of Medicine, Div. of Neurology > >> University of Toronto Faculty of Medicine > >> > >> Kimel Family Building, 6th Floor, Room 644 > >> Baycrest Centre > >> 3560 Bathurst Street > >> Toronto, Ontario M6A 2E1 > >> Canada > >> > >> Phone: 416-785-2500 x3648 > >> Fax: 416-785-2484 > >> Email: jween at klaru-baycrest.on.ca > >> > >> > >> Confidential: This communication and any attachment(s) may contain > >> confidential or privileged information and is intended solely for the > >> address(es) or the entity representing the recipient(s). If you have > >> received this information in error, you are hereby advised to destroy > >> the document and any attachment(s), make no copies of same and inform > >> the sender immediately of the error. Any unauthorized use or > >> disclosure of this information is strictly prohibited. > >> > >> > >> > >> On 11-Feb-09, at 8:21 PM, Andrew Janke wrote: > >> > >>> Hi Jon, > >>> > >>> 2009/2/12 Jon Erik Ween : > >>>> Friends > >>> > >>> Romans... ? > >>> > >>>> I just migrated from Linux to OS X 10.5, but can't figure out how > >>>> to > >>>> set the dynamic linker variables correctly to link to libs in /usr/ > >>>> local and so forth. > >>> > >>> Hrm. Have you got the fink'ish stuff in your .bashrc? > >>> > >>> . /sw/bin/init.sh > >>> > >>> > >>> -- > >>> Andrew Janke > >>> (a.janke at gmail.com || http://a.janke.googlepages.com/) > >>> Canberra->Australia +61 (402) 700 883 > >>> _______________________________________________ > >>> MINC-users at bic.mni.mcgill.ca > >>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > >>> > >> > >> _______________________________________________ > >> MINC-users at bic.mni.mcgill.ca > >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > >> > > > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From dale at bic.mni.mcgill.ca Fri Mar 6 13:01:52 2009 From: dale at bic.mni.mcgill.ca (Dale Einarson) Date: Fri, 6 Mar 2009 13:01:52 -0500 Subject: [MINC-users] dyld errors In-Reply-To: <830390A6-E4E5-4B54-BBD0-A5E20A313C42@umontreal.ca> References: <3865382F-FC0F-4A30-B8EE-EA92F4B8B713@klaru-baycrest.on.ca> <332E7CF0-5D60-45AB-B011-C562F0E32DFF@klaru-baycrest.on.ca> <4BC332FD-0484-4A88-A71C-414F1161E00D@umontreal.ca> <830390A6-E4E5-4B54-BBD0-A5E20A313C42@umontreal.ca> Message-ID: <4C7A9375-0EE5-42EB-A1FA-40A76CDB378F@bic.mni.mcgill.ca> Hello all, Hi Alex, I got this working but (see the quick fix) When I 'setenv DYLD_LIBRARY_PATH ""' I get "dyld: Library not loaded: / libnetpbm.10.dylib". However if I "setenv DYLD_LIBRARY_PATH $LD_LIBRARY_PATH" I get errors about jpeg,tiff and png missing symbols... This is rather odd, the "osx-10.5-x86_64-alex" tar was working last time I installed it... but I just reinstalled it to "see what's up" and found it works if you replace the aforementioned libs with fink ( 32 bit libs )?... A quick fix to get people going? ################################################ # For bash users, this should work #(replace /usr/local the location of the untared copy "osx-10.5- x86_64-alex" ) MINC_ROOT=/usr/local/ # move the libs out of the way ( this means you will need the 3 libs installed via fink) cd $MINC_ROOT mv lib/libJPEG.dylib lib/libJPEG.dylibo mv lib/libTIFF.dylib lib/libTIFF.dylibo mv lib/libPng.dylib lib/libPng.dylibo # set the env to reflect the install export PATH=$MINC_ROOT/bin:$MINC_ROOT/mni/bin:$MINC_ROOT/bic/bin:$PATH export LD_LIBRARY_PATH=/sw/lib:$MINC_ROOT/lib:$MINC_ROOT/mni/lib: $MINC_ROOT/bic/lib export DYLD_LIBRARY_PATH=$LD_LIBRARY_PATH # test to see if it works Display Cheers! dale On 6-Mar-09, at 9:39 AM, Rick Hoge wrote: > > Maybe this is more for the developer's list, but to follow up... > >> The only thing that's missing is an answer to the question "how can I >> tell if my processor is 64-bit". I can't find any command-line >> utility (uname, arch, machine, etc.) that will generate an x86_64 >> output on my MacBook Pro (on which I'm developing and running all >> kinds of 64-bit stuff). > > You *can* get the manufacturer's processor name on the command-line on > a Mac using > > Rick-MBP:~ -> system_profiler | grep 'Processor Name' > Processor Name: Intel Core 2 Duo > > But this does not explicitly indicate the pointer width. > > More painfully, you could build a tiny program that prints the value > of sizeof(void*): > > echo "#include " > test.c > echo "int main(int argc, char *argv[]) { fprintf(stdout,\"%d\n > \",sizeof(void*)); return 0; }" >> test.c > gcc -o test-64 -arch x86_64 test.c > gcc -o test-32 -arch i386 test.c > lipo -create test-64 test-32 -output test-fat > > running the 'test-fat' executable will print 4 on a 32-bit system, and > 8 on a 64-bit system (prints 8 on my Core 2 Duo MacBook Pro). > > The new version of NeuroLens (to be released 'soon') indicates the > architecture in the About panel using something like this. > > Rick > > > > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From dale at bic.mni.mcgill.ca Fri Mar 6 13:46:00 2009 From: dale at bic.mni.mcgill.ca (Dale Einarson) Date: Fri, 6 Mar 2009 13:46:00 -0500 Subject: [MINC-users] compiling dyld, 32, 64? Message-ID: <04CAF529-3FC6-4EA8-A5C0-7EF81E5521C6@bic.mni.mcgill.ca> Hello, Forgive me for starting a new thread but the former seemed to be a couple of separate issue. I built all of he minc tool avail on packages for Mac but not without a lot of pain. I wanted to mention stuff like HDF 1.6.6 getting CPPFLAGS in reverse order... and libtool not getting the "- arch x86_64" arg to gcc, g++ ... Ignorantly, I had built my own version of MINC because I kept getting "wrong architecture" errors form lots of stuff I wanted to build... I now realize that libtool doesn't know that you are trying to build x86_64(see ugly hack below). Would anyone like to share some folklore in regards to building on MacOS? Is there any way to get glibtool to know the *FLAGS from your environment? Sadly I have had to do such ugly hacks as, HDF perl -pi -e 's/-O2 -g x86_64 -arch/-g -O2 -arch x86_64/g' Makefile */ Makefile */*/Makefile */*/*/Makefile LIBTOOL perl -pi -e 's/-fno-builtin/-arch x86_64 -fno-builtin/g' libtool perl -pi -e 's/-dynamiclib/-dynamiclib -arch x86_64/g' libtool ############################ Ricks demo got line wrapped so I have provided a line-wrap'able copy. cat <test.c #include ; int main(int argc, char *argv[]) { fprintf(stdout,"%d\n",sizeof(void*)); return 0; } EOF gcc -o test-64 -arch x86_64 test.c gcc -o test-32 -arch i386 test.c lipo -create test-64 test-32 -output test-fat # # an added toy, just in case you wanted to save bits ;} # arch -arch i386 ./test-fat arch -arch x86_64 ./test-fat Cheers! dale From acveilleux at mrs.mni.mcgill.ca Fri Mar 6 14:09:47 2009 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Fri, 6 Mar 2009 14:09:47 -0500 Subject: [MINC-users] compiling dyld, 32, 64? In-Reply-To: <04CAF529-3FC6-4EA8-A5C0-7EF81E5521C6@bic.mni.mcgill.ca>; from dale@bic.mni.mcgill.ca on Fri, Mar 06, 2009 at 01:46:00PM -0500 References: <04CAF529-3FC6-4EA8-A5C0-7EF81E5521C6@bic.mni.mcgill.ca> Message-ID: <20090306140946.L2730@mrs.mni.mcgill.ca> On Fri, Mar 06, 2009 at 01:46:00PM -0500, Dale Einarson wrote: > > Hello, > Forgive me for starting a new thread but the former seemed to be > a couple of separate issue. > > I built all of he minc tool avail on packages for Mac but not > without a lot of pain. I wanted to mention stuff like HDF 1.6.6 > getting CPPFLAGS in reverse order... and libtool not getting the "- > arch x86_64" arg to gcc, g++ ... Ignorantly, I had built my own > version of MINC because I kept getting "wrong architecture" errors > form lots of stuff I wanted to build... I now realize that libtool > doesn't know that you are trying to build x86_64(see ugly hack below). > > Would anyone like to share some folklore in regards to building > on MacOS? Is there any way to get glibtool to know the *FLAGS from > your environment? I've found that the "correct" solution is usually to rebuild the entire auto* tool chain. With the problems being in the pre-generated shell scripts (like libtool and configure) not being too aware of Mac specificities and often very old. In the case of HDF for example, my expedient "solution" was to run configure on the latest HDF5 package and the 1.6 one and copy the 1.8 libtool in the 1.6 directory. Dirty but it works quickly and it avoids having to hand fix god knows how many build scripts. From memory, most of the minc tools did well with: ./configure --prefix=/usr/local/{mni,bic} CFLAGS="-arch x86_64" CPPFLAGS="-arch x86_64" CXXFLAGS="-arch x86_64" LDFLAGS="-arch x86_64" [--with-minc2] Libraries were more trouble, especially really old ones like IJG's jpeg6b. In at least one case, I hand-linked a library rather then fix the build script (EZTK IIRC, *poke* at Bruce for that...) Hope this helps a bit. Alex From acveilleux at mrs.mni.mcgill.ca Fri Mar 6 14:18:58 2009 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Fri, 6 Mar 2009 14:18:58 -0500 Subject: [MINC-users] dyld errors In-Reply-To: <4C7A9375-0EE5-42EB-A1FA-40A76CDB378F@bic.mni.mcgill.ca>; from dale@bic.mni.mcgill.ca on Fri, Mar 06, 2009 at 01:01:52PM -0500 References: <3865382F-FC0F-4A30-B8EE-EA92F4B8B713@klaru-baycrest.on.ca> <332E7CF0-5D60-45AB-B011-C562F0E32DFF@klaru-baycrest.on.ca> <4BC332FD-0484-4A88-A71C-414F1161E00D@umontreal.ca> <830390A6-E4E5-4B54-BBD0-A5E20A313C42@umontreal.ca> <4C7A9375-0EE5-42EB-A1FA-40A76CDB378F@bic.mni.mcgill.ca> Message-ID: <20090306141858.M2730@mrs.mni.mcgill.ca> On Fri, Mar 06, 2009 at 01:01:52PM -0500, Dale Einarson wrote: > > Hello all, > Hi Alex, I got this working but (see the quick fix) > > When I 'setenv DYLD_LIBRARY_PATH ""' I get "dyld: Library not loaded: / > libnetpbm.10.dylib". However if I "setenv DYLD_LIBRARY_PATH > $LD_LIBRARY_PATH" I get errors about jpeg,tiff and png missing > symbols... Very strange, the build I made comes with its own libnetpbm: mrspc [/usr/local/lib] file libnetpbm.10.26.dylib libnetpbm.10.26.dylib: Mach-O 64-bit dynamically linked shared library x86_64 Of course, I don't have fink in my path at all. Now, I'm a bit behind the curve and I use 10.5.4 on this mac. For the lib you mention, the ones I use are: mrspc [/usr/local/lib] file libpng.3.25.0.dylib libjpeg.62.0.0.dylib libpng12.0.25.0.dylib libtiff.3.dylib libpng.3.25.0.dylib: Mach-O 64-bit dynamically linked shared library x86_64 libjpeg.62.0.0.dylib: Mach-O 64-bit dynamically linked shared library x86_64 libpng12.0.25.0.dylib: Mach-O 64-bit dynamically linked shared library x86_64 libtiff.3.dylib: Mach-O 64-bit dynamically linked shared library x86_64 Perhaps you have two sets of libs co-habitating? > mv lib/libJPEG.dylib lib/libJPEG.dylibo > mv lib/libTIFF.dylib lib/libTIFF.dylibo > mv lib/libPng.dylib lib/libPng.dylibo The capitalization here is quite suspect, this is the format used by the native OSX version of those libs. Now, the mac native version of those libs are only 32-bit... But with the case-preserving/case-insensitive brain damaged HFS+, they can and will overwrite the libs I built. > This is rather odd, the "osx-10.5-x86_64-alex" tar was > working last time I installed it... but I just reinstalled it to "see > what's up" and found it works if you replace the aforementioned libs > with fink ( 32 bit libs )?... It'd be interesting to use DTrace to find out precisely which lib gets open at runtime. Alex From acveilleux at mrs.mni.mcgill.ca Fri Mar 6 14:22:34 2009 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Fri, 6 Mar 2009 14:22:34 -0500 Subject: [MINC-users] compiling dyld, 32, 64? In-Reply-To: <04CAF529-3FC6-4EA8-A5C0-7EF81E5521C6@bic.mni.mcgill.ca>; from dale@bic.mni.mcgill.ca on Fri, Mar 06, 2009 at 01:46:00PM -0500 References: <04CAF529-3FC6-4EA8-A5C0-7EF81E5521C6@bic.mni.mcgill.ca> Message-ID: <20090306142234.N2730@mrs.mni.mcgill.ca> On Fri, Mar 06, 2009 at 01:46:00PM -0500, Dale Einarson wrote: > > Sadly I have had to do such ugly hacks as, > HDF > perl -pi -e 's/-O2 -g x86_64 -arch/-g -O2 -arch x86_64/g' Makefile */ > Makefile */*/Makefile */*/*/Makefile > > LIBTOOL > perl -pi -e 's/-fno-builtin/-arch x86_64 -fno-builtin/g' libtool > perl -pi -e 's/-dynamiclib/-dynamiclib -arch x86_64/g' libtool The following configure line is what I used combined with the libtool hack I mentionned: ./configure CFLAGS="-O2 -arch x86_64 -m64" CXXFLAGS="-O2 -arch x86_64 -m64" --with-szlib=yes --with-zlib=yes --prefix=/usr/local Alex From sean at rogue-research.com Fri Mar 6 14:26:18 2009 From: sean at rogue-research.com (Sean McBride) Date: Fri, 6 Mar 2009 14:26:18 -0500 Subject: [MINC-users] compiling dyld, 32, 64? In-Reply-To: <20090306140946.L2730@mrs.mni.mcgill.ca> References: <04CAF529-3FC6-4EA8-A5C0-7EF81E5521C6@bic.mni.mcgill.ca> <20090306140946.L2730@mrs.mni.mcgill.ca> Message-ID: <20090306192618.1240894215@kingu.local> On 3/6/09 2:09 PM, Alexandre CARMEL-VEILLEUX said: >> Would anyone like to share some folklore in regards to building >> on MacOS? Is there any way to get glibtool to know the *FLAGS from >> your environment? > > I've found that the "correct" solution is usually to rebuild the >entire auto* tool chain. With the problems being in the pre-generated >shell scripts (like libtool and configure) not being too aware of Mac >specificities and often very old. Or, ideally/long term, ditch the entire auto* tool chain in favour of CMake (http://www.cmake.org) which can properly configure/build for Mac, Linux, and Windows. And it properly handles Universal Binaries. MINC2 has some support for CMake, but I don't think it's complete. -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From a.janke at gmail.com Fri Mar 6 18:23:17 2009 From: a.janke at gmail.com (Andrew Janke) Date: Sat, 7 Mar 2009 10:23:17 +1100 Subject: [MINC-users] compiling dyld, 32, 64? In-Reply-To: <20090306192618.1240894215@kingu.local> References: <04CAF529-3FC6-4EA8-A5C0-7EF81E5521C6@bic.mni.mcgill.ca> <20090306140946.L2730@mrs.mni.mcgill.ca> <20090306192618.1240894215@kingu.local> Message-ID: >> ? ? ? I've found that the "correct" solution is usually to rebuild the >>entire auto* tool chain. With the problems being in the pre-generated >>shell scripts (like libtool and configure) not being too aware of Mac >>specificities and often very old. Interesting. The autogen.sh is included though so if you "make distclean" and then autogen/sh things should be OK. > Or, ideally/long term, ditch the entire auto* tool chain in favour of > CMake (http://www.cmake.org) which can properly configure/build for Mac, > Linux, and Windows. But as of yet has very primitive packaging and dist file generation. (CPack). It seems primarily aimed at those who are installing binaries as opposed to libraries + binaries using things like libtool. > ?And it properly handles Universal Binaries. ?MINC2 > has some support for CMake, but I don't think it's complete. Correct, there is a CMakeLists.txt in minc itself that I do keep up to date but that is as far as I got a yonk ago. -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From acveilleux at mrs.mni.mcgill.ca Fri Mar 6 18:34:26 2009 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Fri, 6 Mar 2009 18:34:26 -0500 Subject: [MINC-users] compiling dyld, 32, 64? In-Reply-To: ; from a.janke@gmail.com on Sat, Mar 07, 2009 at 10:23:17AM +1100 References: <04CAF529-3FC6-4EA8-A5C0-7EF81E5521C6@bic.mni.mcgill.ca> <20090306140946.L2730@mrs.mni.mcgill.ca> <20090306192618.1240894215@kingu.local> Message-ID: <20090306183426.D25758@mrs.mni.mcgill.ca> On the CMake front, after much fighting with it, I find that I abhor it and its insistance at wrapping everything in a config file / menu system. I find it very opaque as it insists in implementing its world view on the whole build process. But maybe I just haven't seen the light and my liking the simplicity (or clarity?) of Makefiles. Alex On Sat, Mar 07, 2009 at 10:23:17AM +1100, Andrew Janke wrote: > > Or, ideally/long term, ditch the entire auto* tool chain in favour of > > CMake (http://www.cmake.org) which can properly configure/build for Mac, > > Linux, and Windows. > > But as of yet has very primitive packaging and dist file generation. > (CPack). It seems primarily aimed at those who are installing binaries > as opposed to libraries + binaries using things like libtool. > > > ?And it properly handles Universal Binaries. ?MINC2 > > has some support for CMake, but I don't think it's complete. > > Correct, there is a CMakeLists.txt in minc itself that I do keep up to > date but that is as far as I got a yonk ago. > > > -- > Andrew Janke > (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canberra->Australia +61 (402) 700 883 > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From michel.audette at kitware.com Sat Mar 14 13:20:06 2009 From: michel.audette at kitware.com (Michel Audette) Date: Sat, 14 Mar 2009 10:20:06 -0700 Subject: [MINC-users] digital brain phantom: improved version available publicly? Message-ID: Dear all, I'm aware that Louis Collins had a postdoc a few years back who added detail to the MNI digital brain phantom, and I've been wondering if this highly detailed 2nd revision is available. Does anyone know if there is a version of the atlas that features deep brain structures, or if this one does, in a manner that can replicate for example hypointensity of the subthalamic nucleus in T2 data? In addition, is Remi Kwan's MRI simulator available publicly as well? Cheers, Michel -- Michel Audette, Ph.D. R & D Engineer, Kitware Inc., Chapel Hill, N.C. From se at hst.aau.dk Sat Mar 14 19:55:11 2009 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Sun, 15 Mar 2009 00:55:11 +0100 (CET) Subject: [MINC-users] digital brain phantom: improved version available publicly? In-Reply-To: Message-ID: <529048635.1427461237074911941.JavaMail.root@zimbra-store01.hst.aau.dk> Hi Michel, > In addition, is Remi Kwan's MRI simulator available publicly as well? Yes, the latest version is mrisim-1.0.2 and is available at http://packages.bic.mni.mcgill.ca/ as both source and ubuntu package. Simon From patrick at bic.mni.mcgill.ca Mon Mar 16 16:29:27 2009 From: patrick at bic.mni.mcgill.ca (Patrick Bermudez) Date: Mon, 16 Mar 2009 16:29:27 -0400 Subject: [MINC-users] xdisp problem Message-ID: Dear citizens of MINCdom, I have sucessfully compiled xdisp on two ubuntu hardy systems, one 32-bit and the other 64-bit. xdisp runs well on the 32-bit system but on the 64-bit system I get the following complaint: Font -Adobe-Helvetica-Medium-R-Normal--*-120-*-*-*-*-*-* does not exist Font -*-Courier-Medium-R-Normal--*-120-*-*-*-*-*-* does not exist Font -Adobe-Helvetica-Bold-R-Normal--*-120-*-*-*-*-*-* does not exist Font -Adobe-Times-Bold-I-Normal--*-120-*-*-*-*-*-* does not exist Font 12x24 does not exist font 3 has not been loaded font 4 has not been loaded font 7 has not been loaded font 7 has not been loaded font 3 has not been loaded xdisp: couldn't open 'olgyph-12' font I have noticed this error on other systems (including some of the McBIC boxes). As far as I can tell, I have the same xfonts installed on both setups. Does anyone know a solution/workaround for this? Thanking you muchly in advance. Cheers. Patrick From a.janke at gmail.com Mon Mar 16 19:45:08 2009 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 17 Mar 2009 10:45:08 +1100 Subject: [MINC-users] xdisp problem In-Reply-To: References: Message-ID: Hi Patrick, Have you messed with the xorg.conf on either of the machines? The font path changed from "/usr/share/X11/fonts/..." to "/usr/share/fonts/X11/..." a yonk ago and perhaps this is biting you. Either that or try this: # apt-get install xfs xfstt -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 On Tue, Mar 17, 2009 at 07:29, Patrick Bermudez wrote: > font -Adobe-Helvetica-Medium-R-Normal--*-120-*-*-*-*-*-* does not exist From jween at klaru-baycrest.on.ca Wed Mar 18 23:37:49 2009 From: jween at klaru-baycrest.on.ca (Jon Erik Ween) Date: Wed, 18 Mar 2009 23:37:49 -0400 Subject: [MINC-users] compiling dyld, 32, 64? In-Reply-To: <20090306142234.N2730@mrs.mni.mcgill.ca> References: <04CAF529-3FC6-4EA8-A5C0-7EF81E5521C6@bic.mni.mcgill.ca> <20090306142234.N2730@mrs.mni.mcgill.ca> Message-ID: Friends I gave up trying to compile the visualization tools as all other tools compiled well once I ditched the fink libraries in favor of those in Alex' package, used his configure parameters and figured out to untar in /usr/local (and not in a package directory above that, like one might usually do to segregate stuff). Hence, the lib dependencies were broken. Alex, you may wish to but a line in the README file for noobs like me: "Extract in /usr/local" Anyhow, thanks for all the help from everyone, this is what makes opensource a great place to be! When (if) I find the energy, I'll try building everything from scratch. Cheers Jon Soli Deo Gloria On 6-Mar-09, at 2:22 PM, Alexandre CARMEL-VEILLEUX wrote: > On Fri, Mar 06, 2009 at 01:46:00PM -0500, Dale Einarson wrote: >> >> Sadly I have had to do such ugly hacks as, >> HDF >> perl -pi -e 's/-O2 -g x86_64 -arch/-g -O2 -arch x86_64/g' Makefile >> */ >> Makefile */*/Makefile */*/*/Makefile >> >> LIBTOOL >> perl -pi -e 's/-fno-builtin/-arch x86_64 -fno-builtin/g' libtool >> perl -pi -e 's/-dynamiclib/-dynamiclib -arch x86_64/g' libtool > > The following configure line is what I used combined with the > libtool hack > I mentionned: > > ./configure CFLAGS="-O2 -arch x86_64 -m64" CXXFLAGS="-O2 -arch > x86_64 -m64" --with-szlib=yes --with-zlib=yes --prefix=/usr/local > > Alex > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From jween at klaru-baycrest.on.ca Wed Mar 18 23:44:04 2009 From: jween at klaru-baycrest.on.ca (Jon Erik Ween) Date: Wed, 18 Mar 2009 23:44:04 -0400 Subject: [MINC-users] mincresample center offset Message-ID: Dear minclist friends After a resounding victory over the install/configuration issues in my previous thread, (thanks to help from the list!) I am on to another newbe issue: In trying to register a target brain to an atlas, things get offset (see attached picture), I'm thinking due to something I'm leaving out about world coordinates in creating the transform. What am I missing? Cheers Jon Soli Deo Gloria Here is some info: bash-3.2$ mritoself /usr/local/share/mni_autoreg/ icbm_template_1.00mm_bet.mnc 14017_083005_3dvol_bet.mnc 14017_083005_3dvol bash-3.2$ mincresample -like /usr/local/share/mni_autoreg/ icbm_template_1.00mm_bet.mnc -transform 14017_083005_3dvol.xfm 14017_083005_3dvol_bet.mnc 14017_083005_3dvol_bet_icbm MNI Transform File %Wed Mar 18 22:51:14 2009>>> /usr/local/mni/bin/minctracc /var/folders/ Ph/Ph06bhfiHDWHUvQMhNTgJE++Hbs/-Tmp-/mritoself_7413// icbm_template_1.00mm_bet_crop.mnc /var/folders/Ph/ Ph06bhfiHDWHUvQMhNTgJE++Hbs/-Tmp-/ mritoself_7413//14017_083005_3dvol_bet_crop.mnc 14017_083005_3dvol - est_center -transformation /var/folders/Ph/Ph06bhfiHDWHUvQMhNTgJE+ +Hbs/-Tmp-/mritoself_7413//14017_083005_3dvol_tmp1.xfm -lsq6 -mi - groups 256 -threshold 1195 0 -step 4.3 4.3 4.3 -simplex 1.5 %(Package mni_autoreg 0.99.3, compiled by acveilleux at mrspc.bic.mni.mcgill.ca (i686-apple-darwin9.2.2) on Wed Apr 2 13:09:57 EDT 2008) Transform_Type = Linear; Linear_Transform = 1 0 0 0 0 1 0 0 0 0 1 0; bash-3.2$ mincinfo 14017_083005_3dvol_bet.mnc file: 14017_083005_3dvol_bet.mnc image: signed__ short -32768 to 32767 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 124 1.4 -84.9295 yspace 256 0.859375 -113.669 xspace 256 0.859375 -109.571 bash-3.2$ mincinfo 14017_083005_3dvol_bet_icbm.mnc file: 14017_083005_3dvol_bet_icbm.mnc image: signed__ short -32768 to 32767 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 181 1 0 yspace 217 1 0 xspace 181 1 0 Jon Erik Ween, MD, MS Scientist, Kunin-Lunenfeld Applied Research Unit Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre Assistant Professor, Dept. of Medicine, Div. of Neurology University of Toronto Faculty of Medicine Kimel Family Building, 6th Floor, Room 644 Baycrest Centre 3560 Bathurst Street Toronto, Ontario M6A 2E1 Canada Phone: 416-785-2500 x3648 Fax: 416-785-2484 Email: jween at klaru-baycrest.on.ca Confidential: This communication and any attachment(s) may contain confidential or privileged information and is intended solely for the address(es) or the entity representing the recipient(s). If you have received this information in error, you are hereby advised to destroy the document and any attachment(s), make no copies of same and inform the sender immediately of the error. Any unauthorized use or disclosure of this information is strictly prohibited. From vladimir.fonov at gmail.com Thu Mar 19 00:30:33 2009 From: vladimir.fonov at gmail.com (Vladimir S. Fonov) Date: Thu, 19 Mar 2009 00:30:33 -0400 Subject: [MINC-users] mincresample center offset In-Reply-To: References: Message-ID: <49C1CA69.7030702@gmail.com> Hello , Jon Erik Ween wrote: > In trying to register a target brain to an atlas, things get offset > (see attached picture), I'm thinking due to something I'm leaving out > about world coordinates in creating the transform. What am I missing? Hmmm, no picture? > > bash-3.2$ mritoself /usr/local/share/mni_autoreg/ > icbm_template_1.00mm_bet.mnc 14017_083005_3dvol_bet.mnc > 14017_083005_3dvol mritoself is supposed to be used to register volumes from the same subjects but with different modalities, so probably this is not what you want. Also /usr/local/share/mni_autoreg/icbm_template_1.00mm_bet.mnc doesn't seem to be a valid template. Unless you created it yourself. Standard way of registering to icbm152 template would be like this: mritotal -model icbm_avg_152_t1_tal_lin 14017_083005_3dvol_bet.mnc 14017_083005_3dvol.xfm -- Best regards, Vladimir S. Fonov ~ vladimir.fonov gmail.com From jween at klaru-baycrest.on.ca Thu Mar 19 08:48:29 2009 From: jween at klaru-baycrest.on.ca (Jon Erik Ween) Date: Thu, 19 Mar 2009 08:48:29 -0400 Subject: [MINC-users] mincresample center offset In-Reply-To: <49C1CA69.7030702@gmail.com> References: <49C1CA69.7030702@gmail.com> Message-ID: <95894F6C-B0B0-4EE8-A94F-D1F2D7D4608C@klaru-baycrest.on.ca> Thanks for that, Vladimir. I notice that none of the models/templates are skull stripped. Do you register the native, target MRI (with skull, meninges, etc) with these or an intensity normalized, skull stripped image? Thanks Jon Soli Deo Gloria Jon Erik Ween, MD, MS Scientist, Kunin-Lunenfeld Applied Research Unit Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre Assistant Professor, Dept. of Medicine, Div. of Neurology University of Toronto Faculty of Medicine Kimel Family Building, 6th Floor, Room 644 Baycrest Centre 3560 Bathurst Street Toronto, Ontario M6A 2E1 Canada Phone: 416-785-2500 x3648 Fax: 416-785-2484 Email: jween at klaru-baycrest.on.ca Confidential: This communication and any attachment(s) may contain confidential or privileged information and is intended solely for the address(es) or the entity representing the recipient(s). If you have received this information in error, you are hereby advised to destroy the document and any attachment(s), make no copies of same and inform the sender immediately of the error. Any unauthorized use or disclosure of this information is strictly prohibited. On 19-Mar-09, at 12:30 AM, Vladimir S. Fonov wrote: > Hello , > > Jon Erik Ween wrote: >> In trying to register a target brain to an atlas, things get offset >> (see attached picture), I'm thinking due to something I'm leaving out >> about world coordinates in creating the transform. What am I missing? > Hmmm, no picture? > >> >> bash-3.2$ mritoself /usr/local/share/mni_autoreg/ >> icbm_template_1.00mm_bet.mnc 14017_083005_3dvol_bet.mnc >> 14017_083005_3dvol > > mritoself is supposed to be used to register volumes from the same > subjects but with different modalities, so probably this is not what > you > want. > > Also /usr/local/share/mni_autoreg/icbm_template_1.00mm_bet.mnc doesn't > seem to be a valid template. Unless you created it yourself. > Standard way of registering to icbm152 template would be like this: > > mritotal -model icbm_avg_152_t1_tal_lin 14017_083005_3dvol_bet.mnc > 14017_083005_3dvol.xfm > -- > Best regards, > Vladimir S. Fonov ~ vladimir.fonov gmail.com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Thu Mar 19 08:54:25 2009 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 19 Mar 2009 23:54:25 +1100 Subject: [MINC-users] mincresample center offset In-Reply-To: <95894F6C-B0B0-4EE8-A94F-D1F2D7D4608C@klaru-baycrest.on.ca> References: <49C1CA69.7030702@gmail.com> <95894F6C-B0B0-4EE8-A94F-D1F2D7D4608C@klaru-baycrest.on.ca> Message-ID: On Thu, Mar 19, 2009 at 23:48, Jon Erik Ween wrote: > Thanks for that, Vladimir. I notice that none of the models/templates > are skull stripped. Do you register the native, target ?MRI (with > skull, meninges, etc) with these or an intensity normalized, skull > stripped image? Hi Jon, I take it that you are trying to register skull stripped images with a skull stripped model? In this case what you need to do is to run the script make_model on your stripped model first like this: $ make_model icbm_template_1.00mm_bet Note that the make_model script will expect to find a _mask.mnc and a _headmask.mnc in the same directory. In your case you can probably just copy/modify the icbm ones as you have done already for the model. Have a look in /usr/local/bic/share/mni_autoreg for examples (presuming you have used a package install and/or accepted the defaults when installing). -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From vladimir.fonov at gmail.com Thu Mar 19 09:51:22 2009 From: vladimir.fonov at gmail.com (Vladimir S. Fonov) Date: Thu, 19 Mar 2009 09:51:22 -0400 Subject: [MINC-users] mincresample center offset In-Reply-To: <95894F6C-B0B0-4EE8-A94F-D1F2D7D4608C@klaru-baycrest.on.ca> References: <49C1CA69.7030702@gmail.com> <95894F6C-B0B0-4EE8-A94F-D1F2D7D4608C@klaru-baycrest.on.ca> Message-ID: <49C24DDA.5080705@gmail.com> Hello, Jon Erik Ween wrote: > Thanks for that, Vladimir. I notice that none of the models/templates > are skull stripped. Do you register the native, target MRI (with > skull, meninges, etc) with these or an intensity normalized, skull > stripped image? Yes, usually we do skull stripping after linear registration to the template. You can make a second stage registration to improve it, using only the brain, but then we are usually using brain masks without actually zeroing out the skull in the volume. The standard templates have _mask.mnc files which are brain masks. -- Best regards, Vladimir S. Fonov ~ vladimir.fonov gmail.com From patrick at bic.mni.mcgill.ca Thu Mar 19 13:49:52 2009 From: patrick at bic.mni.mcgill.ca (Patrick Bermudez) Date: Thu, 19 Mar 2009 13:49:52 -0400 Subject: [MINC-users] xdisp problem addendum Message-ID: Thanks for the suggestions Andrew. None of those worked out but they did arouse a suspicion that I had confirmed yesterday. It turns out that the failures have to do with remote X11 display. xdisp works fine when run locally but falls over with the font complaint when using certain X servers under windows. Remote display from most other Linux systems and with OS X 's X11 seems to work fine. This is kind of a dumb reason for a program to fall over but I very much doubt xdisp source code will ever be modified at this point. I just thought I'd post the feedback in case anyone else had this problem. But while on the topic, postf seg faults on remote display from any platform. Anyone know about that? Thanks. Cheers. Patrick > Message: 1 > Date: Mon, 16 Mar 2009 16:29:27 -0400 > From: Patrick Bermudez > Subject: [MINC-users] xdisp problem > To: minc-users at bic.mni.mcgill.ca > Message-ID: > > Content-Type: text/plain; charset=UTF-8 > > Dear citizens of MINCdom, > > I have sucessfully compiled xdisp on two ubuntu hardy systems, one > 32-bit and the other 64-bit. xdisp runs well on the 32-bit system but > on the 64-bit system I get the following complaint: > > Font -Adobe-Helvetica-Medium-R-Normal--*-120-*-*-*-*-*-* does not exist > Font -*-Courier-Medium-R-Normal--*-120-*-*-*-*-*-* does not exist > Font -Adobe-Helvetica-Bold-R-Normal--*-120-*-*-*-*-*-* does not exist > Font -Adobe-Times-Bold-I-Normal--*-120-*-*-*-*-*-* does not exist > Font 12x24 does not exist > font 3 has not been loaded > font 4 has not been loaded > font 7 has not been loaded > font 7 has not been loaded > font 3 has not been loaded > xdisp: couldn't open 'olgyph-12' font > > I have noticed this error on other systems (including some of the > McBIC boxes). As far as I can tell, I have the same xfonts installed > on both setups. Does anyone know a solution/workaround for this? > Thanking you muchly in advance. Cheers. > > Patrick > > > ------------------------------ > > Message: 2 > Date: Tue, 17 Mar 2009 10:45:08 +1100 > From: Andrew Janke > Subject: Re: [MINC-users] xdisp problem > To: MINC users mailing list > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Patrick, > > Have you messed with the xorg.conf on either of the machines? The > font path changed from "/usr/share/X11/fonts/..." to > "/usr/share/fonts/X11/..." a yonk ago and perhaps this is biting you. > > Either that or try this: > > # apt-get install xfs xfstt From acveilleux at mrs.mni.mcgill.ca Thu Mar 19 14:52:26 2009 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Thu, 19 Mar 2009 14:52:26 -0400 Subject: [MINC-users] compiling dyld, 32, 64? In-Reply-To: ; from jween@klaru-baycrest.on.ca on Wed, Mar 18, 2009 at 11:37:49PM -0400 References: <04CAF529-3FC6-4EA8-A5C0-7EF81E5521C6@bic.mni.mcgill.ca> <20090306142234.N2730@mrs.mni.mcgill.ca> Message-ID: <20090319145226.J1314@mrs.mni.mcgill.ca> On Wed, Mar 18, 2009 at 11:37:49PM -0400, Jon Erik Ween wrote: > > I gave up trying to compile the visualization tools as all other tools > compiled well once I ditched the fink libraries in favor of those in > Alex' package, used his configure parameters and figured out to untar > in /usr/local (and not in a package directory above that, like one > might usually do to segregate stuff). Hence, the lib dependencies were > broken. Alex, you may wish to but a line in the README file for noobs > like me: > > "Extract in /usr/local" The alternative is to setup your environment DYLD_LIBRARY_PATH. Suppose you untared my package in /opt/local (csh:) setenv DYLD_LIBRARY_PATH "/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources:/opt/local/lib:${DYLD_LIBRARY_PATH}" (bash:) export DYLD_LIBRARY_PATH="/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources:/opt/local/lib:${DYLD_LIBRARY_PATH}" The first item in the DYLD_LIBRARY_PATH should resolve the infamous libJPEG problem. It seems that ld will scan all those dirs, figure out the difference between libJPEG.dylib and libjpeg.dylib and use the right one (so ld on mac is case-sensite/case-preserving internally). Alex > > Anyhow, thanks for all the help from everyone, this is what makes > opensource a great place to be! When (if) I find the energy, I'll try > building everything from scratch. > > Cheers > > Jon > > Soli Deo Gloria > > > On 6-Mar-09, at 2:22 PM, Alexandre CARMEL-VEILLEUX wrote: > > > On Fri, Mar 06, 2009 at 01:46:00PM -0500, Dale Einarson wrote: > >> > >> Sadly I have had to do such ugly hacks as, > >> HDF > >> perl -pi -e 's/-O2 -g x86_64 -arch/-g -O2 -arch x86_64/g' Makefile > >> */ > >> Makefile */*/Makefile */*/*/Makefile > >> > >> LIBTOOL > >> perl -pi -e 's/-fno-builtin/-arch x86_64 -fno-builtin/g' libtool > >> perl -pi -e 's/-dynamiclib/-dynamiclib -arch x86_64/g' libtool > > > > The following configure line is what I used combined with the > > libtool hack > > I mentionned: > > > > ./configure CFLAGS="-O2 -arch x86_64 -m64" CXXFLAGS="-O2 -arch > > x86_64 -m64" --with-szlib=yes --with-zlib=yes --prefix=/usr/local > > > > Alex > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From drew.morris at sickkids.ca Fri Mar 20 16:36:01 2009 From: drew.morris at sickkids.ca (drew.morris at sickkids.ca) Date: Fri, 20 Mar 2009 16:36:01 -0400 Subject: [MINC-users] inter-slice registration? Message-ID: Is there any program, or suggested combinations of programs in the minc toolkit to handle interslice registration? In my EPI volumes (from DTI), I'm seeing that slice n seems to be rotated away from slice n+1, e.g. I'd like to rotate them into alignment. Thanks for any advice and apologies if this question has been posted several times before. Drew From a.janke at gmail.com Mon Mar 23 06:59:05 2009 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 23 Mar 2009 21:59:05 +1100 Subject: [MINC-users] digital brain phantom: improved version available publicly? In-Reply-To: References: Message-ID: Hi Michel, > I'm aware that Louis Collins had a postdoc a few years back who added detail > to the MNI digital brain phantom, and I've been wondering if this highly > detailed 2nd revision is available. Does anyone know if there is a version > of the atlas that features deep brain structures, or if this one does, in a > manner that can replicate for example hypointensity of the subthalamic > nucleus in T2 data? The postdoc in question was Berengere from Louis' lab. I have no idea if it was released or not but I do know that some of it made its way into brainweb. -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From jween at klaru-baycrest.on.ca Wed Mar 25 12:18:40 2009 From: jween at klaru-baycrest.on.ca (Jon Erik Ween) Date: Wed, 25 Mar 2009 12:18:40 -0400 Subject: [MINC-users] Classify In-Reply-To: <49C24DDA.5080705@gmail.com> References: <49C1CA69.7030702@gmail.com> <95894F6C-B0B0-4EE8-A94F-D1F2D7D4608C@klaru-baycrest.on.ca> <49C24DDA.5080705@gmail.com> Message-ID: Dear minclist. Sorry for the incremental posts, but then, how is one to learn?? Anyway, thanks to help from the list, I'm now in the possession of skull-stripped, talairach registered, lesion masked 3DT1 images of a group of patients and would like to tissue classify these volumes (and hopefully label major lobes etc) so I can calculate tissue and lesion volumes (globally and in particular lobes, etc). Running "classify" (or classify_clean, I can't figure out the difference between these two, exactly) complains that I don't have a tag file (or in the case of classify_clean, that the tags are not in the volume). I was thinking that "classify" used the specified model to figure out which voxels were which tissue, or do I need to manually tag voxels in each of the target volumes? I, again, appreciate any guidance! Cheers Jon Soli Deo Gloria Jon Erik Ween, MD, MS Scientist, Kunin-Lunenfeld Applied Research Unit Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre Assistant Professor, Dept. of Medicine, Div. of Neurology University of Toronto Faculty of Medicine Kimel Family Building, 6th Floor, Room 644 Baycrest Centre 3560 Bathurst Street Toronto, Ontario M6A 2E1 Canada Phone: 416-785-2500 x3648 Fax: 416-785-2484 Email: jween at klaru-baycrest.on.ca Confidential: This communication and any attachment(s) may contain confidential or privileged information and is intended solely for the address(es) or the entity representing the recipient(s). If you have received this information in error, you are hereby advised to destroy the document and any attachment(s), make no copies of same and inform the sender immediately of the error. Any unauthorized use or disclosure of this information is strictly prohibited. From jason at bic.mni.mcgill.ca Wed Mar 25 12:51:04 2009 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Wed, 25 Mar 2009 12:51:04 -0400 Subject: [MINC-users] Classify In-Reply-To: References: Message-ID: <261E465A-4DBE-4F2B-B950-1CA10C9EF89F@bic.mni.mcgill.ca> Hi Jon, classify is based on using a training set to initialize the tissue classification - either based on probability maps or on manually selected tags. In other words, you could use Display to pick 100 points or so that you think are grey matter, 100 that are white matter, etc., then use that to initialize the classification of every voxel. Once you've trained the classifier once you can also save the training data and apply it to new volumes without repicking individual points (though this is quite scanner specific - i.e. it usually works for one sequence from one site, not across sequences or sites - for that probability maps are better). classify_clean uses classify but prunes those initial points first to remove any outliers - this can be a benefit when you use spatial priors based on probability maps. Hope this helps, Jason On 25-Mar-09, at 12:18 PM, Jon Erik Ween wrote: > Dear minclist. > > Sorry for the incremental posts, but then, how is one to learn?? > > Anyway, thanks to help from the list, I'm now in the possession of > skull-stripped, talairach registered, lesion masked 3DT1 images of a > group of patients and would like to tissue classify these volumes (and > hopefully label major lobes etc) so I can calculate tissue and lesion > volumes (globally and in particular lobes, etc). Running > "classify" (or classify_clean, I can't figure out the difference > between these two, exactly) complains that I don't have a tag file (or > in the case of classify_clean, that the tags are not in the volume). I > was thinking that "classify" used the specified model to figure out > which voxels were which tissue, or do I need to manually tag voxels in > each of the target volumes? > > I, again, appreciate any guidance! > > Cheers > > Jon > > Soli Deo Gloria > > Jon Erik Ween, MD, MS > Scientist, Kunin-Lunenfeld Applied Research Unit > Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre > Assistant Professor, Dept. of Medicine, Div. of Neurology > University of Toronto Faculty of Medicine > > Kimel Family Building, 6th Floor, Room 644 > Baycrest Centre > 3560 Bathurst Street > Toronto, Ontario M6A 2E1 > Canada > > Phone: 416-785-2500 x3648 > Fax: 416-785-2484 > Email: jween at klaru-baycrest.on.ca > > > Confidential: This communication and any attachment(s) may contain > confidential or privileged information and is intended solely for the > address(es) or the entity representing the recipient(s). If you have > received this information in error, you are hereby advised to destroy > the document and any attachment(s), make no copies of same and inform > the sender immediately of the error. Any unauthorized use or > disclosure of this information is strictly prohibited. > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From jween at klaru-baycrest.on.ca Thu Mar 26 08:39:50 2009 From: jween at klaru-baycrest.on.ca (Jon Erik Ween) Date: Thu, 26 Mar 2009 08:39:50 -0400 Subject: [MINC-users] Classify In-Reply-To: <261E465A-4DBE-4F2B-B950-1CA10C9EF89F@bic.mni.mcgill.ca> References: <261E465A-4DBE-4F2B-B950-1CA10C9EF89F@bic.mni.mcgill.ca> Message-ID: <23260401-4B6F-48BD-8601-D27C94E28AE3@klaru-baycrest.on.ca> Thanks Jason So, I tag 100 white matter, 100 grey [cortical and deep] voxels, fairly evenly distributed throughout the brain) using Display, with different label values for each tissue type (does the value matter?) and save as a .tag file? You do this on the intensity normalized volume and not the native image, right? Is this process sensitive to changes in scanner software? We upgrade the magnets from time to time. Where do I find an appropriate probability maps? I'm supposing the MNI averages are not the ones. Do the autoreg models work for this? Thanks Jon Soli Deo Gloria Jon Erik Ween, MD, MS Scientist, Kunin-Lunenfeld Applied Research Unit Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre Assistant Professor, Dept. of Medicine, Div. of Neurology University of Toronto Faculty of Medicine Kimel Family Building, 6th Floor, Room 644 Baycrest Centre 3560 Bathurst Street Toronto, Ontario M6A 2E1 Canada Phone: 416-785-2500 x3648 Fax: 416-785-2484 Email: jween at klaru-baycrest.on.ca Confidential: This communication and any attachment(s) may contain confidential or privileged information and is intended solely for the address(es) or the entity representing the recipient(s). If you have received this information in error, you are hereby advised to destroy the document and any attachment(s), make no copies of same and inform the sender immediately of the error. Any unauthorized use or disclosure of this information is strictly prohibited. On 25-Mar-09, at 12:51 PM, Jason Lerch wrote: > Hi Jon, > > classify is based on using a training set to initialize the tissue > classification - either based on probability maps or on manually > selected tags. In other words, you could use Display to pick 100 > points or so that you think are grey matter, 100 that are white > matter, etc., then use that to initialize the classification of every > voxel. Once you've trained the classifier once you can also save the > training data and apply it to new volumes without repicking individual > points (though this is quite scanner specific - i.e. it usually works > for one sequence from one site, not across sequences or sites - for > that probability maps are better). > > classify_clean uses classify but prunes those initial points first to > remove any outliers - this can be a benefit when you use spatial > priors based on probability maps. > > Hope this helps, > > Jason > > > > > On 25-Mar-09, at 12:18 PM, Jon Erik Ween wrote: > >> Dear minclist. >> >> Sorry for the incremental posts, but then, how is one to learn?? >> >> Anyway, thanks to help from the list, I'm now in the possession of >> skull-stripped, talairach registered, lesion masked 3DT1 images of a >> group of patients and would like to tissue classify these volumes >> (and >> hopefully label major lobes etc) so I can calculate tissue and lesion >> volumes (globally and in particular lobes, etc). Running >> "classify" (or classify_clean, I can't figure out the difference >> between these two, exactly) complains that I don't have a tag file >> (or >> in the case of classify_clean, that the tags are not in the >> volume). I >> was thinking that "classify" used the specified model to figure out >> which voxels were which tissue, or do I need to manually tag voxels >> in >> each of the target volumes? >> >> I, again, appreciate any guidance! >> >> Cheers >> >> Jon >> >> Soli Deo Gloria >> >> Jon Erik Ween, MD, MS >> Scientist, Kunin-Lunenfeld Applied Research Unit >> Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre >> Assistant Professor, Dept. of Medicine, Div. of Neurology >> University of Toronto Faculty of Medicine >> >> Kimel Family Building, 6th Floor, Room 644 >> Baycrest Centre >> 3560 Bathurst Street >> Toronto, Ontario M6A 2E1 >> Canada >> >> Phone: 416-785-2500 x3648 >> Fax: 416-785-2484 >> Email: jween at klaru-baycrest.on.ca >> >> >> Confidential: This communication and any attachment(s) may contain >> confidential or privileged information and is intended solely for the >> address(es) or the entity representing the recipient(s). If you have >> received this information in error, you are hereby advised to destroy >> the document and any attachment(s), make no copies of same and inform >> the sender immediately of the error. Any unauthorized use or >> disclosure of this information is strictly prohibited. >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From jason at bic.mni.mcgill.ca Thu Mar 26 09:56:03 2009 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Thu, 26 Mar 2009 09:56:03 -0400 Subject: [MINC-users] Classify In-Reply-To: <23260401-4B6F-48BD-8601-D27C94E28AE3@klaru-baycrest.on.ca> References: Message-ID: <062BF6A5-0E8C-427A-BFF6-506BAB53457E@bic.mni.mcgill.ca> On 26-Mar-09, at 8:39 AM, Jon Erik Ween wrote: > Thanks Jason > > So, I tag 100 white matter, 100 grey [cortical and deep] voxels, > fairly evenly distributed throughout the brain) using Display, with > different label values for each tissue type (does the value matter?) > and save as a .tag file? That looks correct - and yes, the value does matter: you want it to be an integer which will give the corresponding value to the classified file. We usually use 0 for background, 1 for CSF, 2, for WM, 3 for GM. But that's merely convention - though a few scripts assume these values. > > > You do this on the intensity normalized volume and not the native > image, right? Yup. > > > Is this process sensitive to changes in scanner software? We upgrade > the magnets from time to time. If you pick tags each time then it is not sensitive to scanner software. If you train a classifier and reuse it then it is sensitive to scanner software (maybe - depends on whether the upgrade affected signal intensities with the sequence you are using). If you use spatial priors then it is once again not sensitive to scanner software. > > > Where do I find an appropriate probability maps? The probability maps are not distributed by the MNI as far as I can tell - but the spatial priors derived from those probability maps are part of the classify packages (see models/ntags_1000_bg.tag). These assume alignment to the MNI version of Talairach space - you ought to be able to use these without modification. They are based on 1000 points per tissue class, each point having a 90% or greater likelihood of being of that tissue type. If you want the probability maps themselves you'll have to contact somebody at the MNI (Alex Zijdenbos, I suppose). It's also not too hard to generate the probability maps yourself - classify a bunch of scans, separate out the individual tissue types, then use mincaverage on the binary maps to create your probability map. Once you have that you can use the extracttag command to get your tag point set. Cheers, Jason > I'm supposing the MNI > averages are not the ones. Do the autoreg models work for this? > > Thanks > > Jon > > Soli Deo Gloria > > Jon Erik Ween, MD, MS > Scientist, Kunin-Lunenfeld Applied Research Unit > Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre > Assistant Professor, Dept. of Medicine, Div. of Neurology > University of Toronto Faculty of Medicine > > Kimel Family Building, 6th Floor, Room 644 > Baycrest Centre > 3560 Bathurst Street > Toronto, Ontario M6A 2E1 > Canada > > Phone: 416-785-2500 x3648 > Fax: 416-785-2484 > Email: jween at klaru-baycrest.on.ca > > > Confidential: This communication and any attachment(s) may contain > confidential or privileged information and is intended solely for the > address(es) or the entity representing the recipient(s). If you have > received this information in error, you are hereby advised to destroy > the document and any attachment(s), make no copies of same and inform > the sender immediately of the error. Any unauthorized use or > disclosure of this information is strictly prohibited. > > > > On 25-Mar-09, at 12:51 PM, Jason Lerch wrote: > >> Hi Jon, >> >> classify is based on using a training set to initialize the tissue >> classification - either based on probability maps or on manually >> selected tags. In other words, you could use Display to pick 100 >> points or so that you think are grey matter, 100 that are white >> matter, etc., then use that to initialize the classification of every >> voxel. Once you've trained the classifier once you can also save the >> training data and apply it to new volumes without repicking >> individual >> points (though this is quite scanner specific - i.e. it usually works >> for one sequence from one site, not across sequences or sites - for >> that probability maps are better). >> >> classify_clean uses classify but prunes those initial points first to >> remove any outliers - this can be a benefit when you use spatial >> priors based on probability maps. >> >> Hope this helps, >> >> Jason >> >> >> >> >> On 25-Mar-09, at 12:18 PM, Jon Erik Ween wrote: >> >>> Dear minclist. >>> >>> Sorry for the incremental posts, but then, how is one to learn?? >>> >>> Anyway, thanks to help from the list, I'm now in the possession of >>> skull-stripped, talairach registered, lesion masked 3DT1 images of a >>> group of patients and would like to tissue classify these volumes >>> (and >>> hopefully label major lobes etc) so I can calculate tissue and >>> lesion >>> volumes (globally and in particular lobes, etc). Running >>> "classify" (or classify_clean, I can't figure out the difference >>> between these two, exactly) complains that I don't have a tag file >>> (or >>> in the case of classify_clean, that the tags are not in the >>> volume). I >>> was thinking that "classify" used the specified model to figure out >>> which voxels were which tissue, or do I need to manually tag voxels >>> in >>> each of the target volumes? >>> >>> I, again, appreciate any guidance! >>> >>> Cheers >>> >>> Jon >>> >>> Soli Deo Gloria >>> >>> Jon Erik Ween, MD, MS >>> Scientist, Kunin-Lunenfeld Applied Research Unit >>> Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre >>> Assistant Professor, Dept. of Medicine, Div. of Neurology >>> University of Toronto Faculty of Medicine >>> >>> Kimel Family Building, 6th Floor, Room 644 >>> Baycrest Centre >>> 3560 Bathurst Street >>> Toronto, Ontario M6A 2E1 >>> Canada >>> >>> Phone: 416-785-2500 x3648 >>> Fax: 416-785-2484 >>> Email: jween at klaru-baycrest.on.ca >>> >>> >>> Confidential: This communication and any attachment(s) may contain >>> confidential or privileged information and is intended solely for >>> the >>> address(es) or the entity representing the recipient(s). If you have >>> received this information in error, you are hereby advised to >>> destroy >>> the document and any attachment(s), make no copies of same and >>> inform >>> the sender immediately of the error. Any unauthorized use or >>> disclosure of this information is strictly prohibited. >>> _______________________________________________ >>> MINC-users at bic.mni.mcgill.ca >>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From claude at bic.mni.mcgill.ca Thu Mar 26 10:10:29 2009 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Thu, 26 Mar 2009 10:10:29 -0400 Subject: [MINC-users] Classify In-Reply-To: <062BF6A5-0E8C-427A-BFF6-506BAB53457E@bic.mni.mcgill.ca> Message-ID: <200903261410.n2QEATDP028660@grumio.bic.mni.mcgill.ca> > That looks correct - and yes, the value does matter: you want it to be > an integer which will give the corresponding value to the classified > file. We usually use 0 for background, 1 for CSF, 2, for WM, 3 for GM. > But that's merely convention - though a few scripts assume these values. Jason, Isn't it GM=2 and WM=3? Claude From jason at bic.mni.mcgill.ca Thu Mar 26 10:14:01 2009 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Thu, 26 Mar 2009 10:14:01 -0400 Subject: [MINC-users] Classify In-Reply-To: <200903261410.n2QEATDP028660@grumio.bic.mni.mcgill.ca> References: <200903261410.n2QEATDP028660@grumio.bic.mni.mcgill.ca> Message-ID: On 26-Mar-09, at 10:10 AM, Claude LEPAGE wrote: >> That looks correct - and yes, the value does matter: you want it to >> be >> an integer which will give the corresponding value to the classified >> file. We usually use 0 for background, 1 for CSF, 2, for WM, 3 for >> GM. >> But that's merely convention - though a few scripts assume these >> values. > > Jason, > > Isn't it GM=2 and WM=3? Right you are - my bad. > > > Claude > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From jween at klaru-baycrest.on.ca Mon Mar 30 16:23:43 2009 From: jween at klaru-baycrest.on.ca (Jon Erik Ween) Date: Mon, 30 Mar 2009 16:23:43 -0400 Subject: [MINC-users] compiling dyld, 32, 64? In-Reply-To: <20090306142234.N2730@mrs.mni.mcgill.ca> References: <04CAF529-3FC6-4EA8-A5C0-7EF81E5521C6@bic.mni.mcgill.ca> <20090306142234.N2730@mrs.mni.mcgill.ca> Message-ID: <1AE3E552-EEFF-4351-BA67-81AF54C8A983@klaru-baycrest.on.ca> Alex I noticed some odd behavior with the 64 bit OSS X version of Display: If I move Display's "keyboard" function-controller window, it stops responding to mouse clicks and keyboard strokes. As long as I lave it alone, everything seems to work well. Is that odd? Jon Soli Deo Gloria Jon Erik Ween, MD, MS Scientist, Kunin-Lunenfeld Applied Research Unit Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre Assistant Professor, Dept. of Medicine, Div. of Neurology University of Toronto Faculty of Medicine Kimel Family Building, 6th Floor, Room 644 Baycrest Centre 3560 Bathurst Street Toronto, Ontario M6A 2E1 Canada Phone: 416-785-2500 x3648 Fax: 416-785-2484 Email: jween at klaru-baycrest.on.ca Confidential: This communication and any attachment(s) may contain confidential or privileged information and is intended solely for the address(es) or the entity representing the recipient(s). If you have received this information in error, you are hereby advised to destroy the document and any attachment(s), make no copies of same and inform the sender immediately of the error. Any unauthorized use or disclosure of this information is strictly prohibited. On 6-Mar-09, at 2:22 PM, Alexandre CARMEL-VEILLEUX wrote: > On Fri, Mar 06, 2009 at 01:46:00PM -0500, Dale Einarson wrote: >> >> Sadly I have had to do such ugly hacks as, >> HDF >> perl -pi -e 's/-O2 -g x86_64 -arch/-g -O2 -arch x86_64/g' Makefile >> */ >> Makefile */*/Makefile */*/*/Makefile >> >> LIBTOOL >> perl -pi -e 's/-fno-builtin/-arch x86_64 -fno-builtin/g' libtool >> perl -pi -e 's/-dynamiclib/-dynamiclib -arch x86_64/g' libtool > > The following configure line is what I used combined with the > libtool hack > I mentionned: > > ./configure CFLAGS="-O2 -arch x86_64 -m64" CXXFLAGS="-O2 -arch > x86_64 -m64" --with-szlib=yes --with-zlib=yes --prefix=/usr/local > > Alex > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From dale at bic.mni.mcgill.ca Mon Mar 30 17:01:59 2009 From: dale at bic.mni.mcgill.ca (Dale Einarson) Date: Mon, 30 Mar 2009 17:01:59 -0400 Subject: [MINC-users] compiling dyld, 32, 64? In-Reply-To: <1AE3E552-EEFF-4351-BA67-81AF54C8A983@klaru-baycrest.on.ca> References: <04CAF529-3FC6-4EA8-A5C0-7EF81E5521C6@bic.mni.mcgill.ca> <20090306142234.N2730@mrs.mni.mcgill.ca> <1AE3E552-EEFF-4351-BA67-81AF54C8A983@klaru-baycrest.on.ca> Message-ID: <7F295845-9A64-4539-9612-EAA13D1844BF@bic.mni.mcgill.ca> Hi all, I haven't seen this bug yet but just in case... Do note that there are both minc1 and minc2 version of Display in that tarball... minc1 mni/bin/display minc2 bic/bin/Display Cheers! dale On 30-Mar-09, at 4:23 PM, Jon Erik Ween wrote: > Alex > > I noticed some odd behavior with the 64 bit OSS X version of Display: > If I move Display's "keyboard" function-controller window, it stops > responding to mouse clicks and keyboard strokes. As long as I lave it > alone, everything seems to work well. Is that odd? > > Jon > > Soli Deo Gloria > > Jon Erik Ween, MD, MS > Scientist, Kunin-Lunenfeld Applied Research Unit > Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre > Assistant Professor, Dept. of Medicine, Div. of Neurology > University of Toronto Faculty of Medicine > > Kimel Family Building, 6th Floor, Room 644 > Baycrest Centre > 3560 Bathurst Street > Toronto, Ontario M6A 2E1 > Canada > > Phone: 416-785-2500 x3648 > Fax: 416-785-2484 > Email: jween at klaru-baycrest.on.ca > > > Confidential: This communication and any attachment(s) may contain > confidential or privileged information and is intended solely for the > address(es) or the entity representing the recipient(s). If you have > received this information in error, you are hereby advised to destroy > the document and any attachment(s), make no copies of same and inform > the sender immediately of the error. Any unauthorized use or > disclosure of this information is strictly prohibited. > > > > On 6-Mar-09, at 2:22 PM, Alexandre CARMEL-VEILLEUX wrote: > >> On Fri, Mar 06, 2009 at 01:46:00PM -0500, Dale Einarson wrote: >>> >>> Sadly I have had to do such ugly hacks as, >>> HDF >>> perl -pi -e 's/-O2 -g x86_64 -arch/-g -O2 -arch x86_64/g' Makefile >>> */ >>> Makefile */*/Makefile */*/*/Makefile >>> >>> LIBTOOL >>> perl -pi -e 's/-fno-builtin/-arch x86_64 -fno-builtin/g' libtool >>> perl -pi -e 's/-dynamiclib/-dynamiclib -arch x86_64/g' libtool >> >> The following configure line is what I used combined with the >> libtool hack >> I mentionned: >> >> ./configure CFLAGS="-O2 -arch x86_64 -m64" CXXFLAGS="-O2 -arch >> x86_64 -m64" --with-szlib=yes --with-zlib=yes --prefix=/usr/local >> >> Alex >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From jween at klaru-baycrest.on.ca Mon Mar 30 17:59:54 2009 From: jween at klaru-baycrest.on.ca (Jon Erik Ween) Date: Mon, 30 Mar 2009 17:59:54 -0400 Subject: [MINC-users] Classify In-Reply-To: References: <200903261410.n2QEATDP028660@grumio.bic.mni.mcgill.ca> Message-ID: <3B76FBAC-57FF-45EA-8A16-4507E2C42690@klaru-baycrest.on.ca> May I trouble the list with another question? (Guess I'll do so anyhow...) So, I've created a tagfile with some classifications that seem reasonable, BUT, Display didn't seem to want to record tags with value"0", hence Background is labeled as CSF in the next step. What am I missing here? I set the user_mask_value below to "0" as my mask is a lesion mask which I don't want to classify. (Picture1) Then, I feed classify with the following: bash-3.2$ classify -clobber -user_mask_value 0 -tagfile tags.tag -mask 14017_083005_combo_lbl2_tal.mnc 14017_083005_3dvol_tal.mnc 14017_083005_3dvol_cls.mnc and get the attached output in Picture2. This procedure still over-classifies grey matter volumes by including the lesion areas that I was trying to mask out. How come? Cheers! Jon Soli Deo Gloria On 26-Mar-09, at 10:14 AM, Jason Lerch wrote: > > On 26-Mar-09, at 10:10 AM, Claude LEPAGE wrote: > >>> That looks correct - and yes, the value does matter: you want it to >>> be >>> an integer which will give the corresponding value to the classified >>> file. We usually use 0 for background, 1 for CSF, 2, for WM, 3 for >>> GM. >>> But that's merely convention - though a few scripts assume these >>> values. >> >> Jason, >> >> Isn't it GM=2 and WM=3? > > Right you are - my bad. > >> >> >> Claude >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users >