Freesurfer June 2008

freesurfer@nmr.mgh.harvard.edu

58 participants
77 discussions

mri_convert from BRIK to NIFTI
by Lauren Ethridge 19 Jun '08

19 Jun '08

Hi, I'm relatively new to freesurfer, just learned about it at the Multi-modal course this year, and I'm trying to apply it to some of our own functional data. This may be a bit of a simple question, but here goes. I've tried to use mri_convert to change a brik file to nifti but I get the following error: [quackers@matlab anat_lauren]$ mri_convert fa+orig.BRIK fa.nii mri_convert fa+orig.BRIK fa.nii $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from fa+orig.BRIK... afniRead(): error opening file /birc/jemlab/anat_lauren/fa+orig.HEAD [quackers@matlab anat_lauren]$ The header file is located in the same folder as the brik file. Is there something I need to do to the header file in order to make it readable to fsfast? I've also tried using unpacksdcmdir to unpack the raw dicom files, but the data came from a GE scanner so it doesn't seem to recognize them. Any help would be much appreciated. Lauren ------ Lauren Ethridge Graduate Student - Neuroscience Franklin Foundation Fellow Biomedical and Health Sciences Institute University of Georgia 706-542-3128

2 1

questions regarding freesurfer 4.0.5
by Sebastian Moeller 19 Jun '08

19 Jun '08

First, if this shows up twice, let m apologise for mixing up my email addresses... Aloha fellow surfers, I just installed ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Darwin-leopard-i686-st… on my: intel macbook, running 10.5.3 with 4GB of RAM. A few observations: 1) minor: freeview does not seem to be part of the dmg, probably expected, but from the release notes it is not obvious, whether the macos version should contain it or not 2) minor, minor: it seems like the whole macos version is built for 32bit only (at least that is what "file `which mri_convert`" and a few other binaries tell me); would it be possible to have a 64bit built (than my macbook might suffice for surface reconstruction as well). 3) scuba dies horribly (tkmedit and tksurfer, however seem to work, at least they start up and display something), here is the problem report: Path: /opt/freesurfer//bin/scuba.bin Identifier: scuba.bin Version: ??? (???) Code Type: X86 (Native) Parent Process: tcsh [18243] Date/Time: 2008-06-18 10:10:42.832 +0200 OS Version: Mac OS X 10.5.3 (9D34) Report Version: 6 Exception Type: EXC_BAD_ACCESS (SIGBUS) Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000000000000 Crashed Thread: 0 Thread 0 Crashed: 0 scuba.bin 0x001e5764 0x1000 + 1984356 1 dyld 0x8fe0e723 ImageLoader::recursiveInitialization(ImageLoader::LinkContext const&, unsigned int) + 307 2 dyld 0x8fe0e809 ImageLoader::runInitializers(ImageLoader::LinkContext const&) + 57 3 dyld 0x8fe04102 dyld::initializeMainExecutable() + 146 4 dyld 0x8fe07b5f dyld::_main(mach_header const*, unsigned long, int, char const**, char const**, char const**) + 2975 5 dyld 0x8fe01872 dyldbootstrap::start(mach_header const*, int, char const**, long) + 818 6 dyld 0x8fe01037 _dyld_start + 39 Thread 0 crashed with X86 Thread State (32-bit): eax: 0x00000000 ebx: 0x001e570c ecx: 0x00000002 edx: 0x00000000 edi: 0x00000026 esi: 0x00001000 ebp: 0xbfffd548 esp: 0xbfffd4c0 ss: 0x0000001f efl: 0x00010282 eip: 0x001e5764 cs: 0x00000017 ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037 cr2: 0x00000000 Binary Images: 0x1000 - 0x23ffed +scuba.bin ??? (???) <d06ab65353013407522c78a886efea54> /opt/freesurfer/bin/scuba.bin 0x2af000 - 0x35ffe9 +libGLU.1.dylib ??? (???) /usr/X11/lib/libGLU. 1.dylib 0x37a000 - 0x38efe7 +libXmu.6.dylib ??? (???) <4368a7afa86da654c52e64ba19a9097b> /usr/X11/lib/libXmu.6.dylib 0x397000 - 0x3e2ff8 +libXt.6.dylib ??? (???) <d700ce75d38c60146177b10c3883f10d> /usr/X11/lib/libXt.6.dylib 0x3f7000 - 0x3fcffc +libSM.6.dylib ??? (???) <1a5a19fa53bdce9d344782a05db3c4e7> /usr/X11/lib/libSM.6.dylib 0x402000 - 0x413ff7 +libICE.6.dylib ??? (???) <0ed3bdd6f53b07a00ef27fc3577f283a> /usr/X11/lib/libICE.6.dylib 0x41c000 - 0x428ffa +libXext.6.dylib ??? (???) <a94a1adf7793da948691b99b4777e2e1> /usr/X11/lib/libXext.6.dylib 0x430000 - 0x51bfe7 +libX11.6.dylib ??? (???) <cc5a62e8982326ffe327eafb901129d3> /usr/X11/lib/libX11.6.dylib 0x53d000 - 0x53ffef +libXdmcp.6.dylib ??? (???) <6f2b16b27bab3a08bd635d8e56bfe9f6> /usr/X11/lib/libXdmcp.6.dylib 0x544000 - 0x544ff1 +libXau.6.dylib ??? (???) <cd091bf5ae82c18ee03a9b4f6bb93d57> /usr/X11/lib/libXau.6.dylib 0x549000 - 0x596fe7 +libGL.1.dylib ??? (???) <f96baeea46fa05910212d7427da5f33a> /usr/X11/lib/libGL.1.dylib 0x5c3000 - 0x5cefeb libXplugin.1.dylib ??? (???) <b175d293d67060cbf50aa111b2ab41b0> /usr/lib/libXplugin.1.dylib 0x5d7000 - 0x5edfe7 com.apple.CoreVideo 1.5.1 (1.5.1) <ed7bb95fb94817ea3212090aac5c65f3> /System/Library/Frameworks/ CoreVideo.framework/Versions/A/CoreVideo 0xa000000 - 0xa07cfef +libtcl8.4.dylib ??? (???) /opt/freesurfer/lib/ tcltktixblt/lib/libtcl8.4.dylib 0xb000000 - 0xb0a4fff +libtk8.4.dylib ??? (???) <09a6ab5749f362ad8838bfe610a8f33f> /opt/freesurfer/lib/tcltktixblt/lib/ libtk8.4.dylib 0x8fe00000 - 0x8fe2da53 dyld 96.2 (???) <5013f43c4d2c33c9619011f103ec3238> /usr/lib/dyld 0x90003000 - 0x902ddff3 com.apple.CoreServices.CarbonCore 786.4 (786.4) <059c4803a7a95e3c1a95a332baeb1edf> /System/Library/Frameworks/ CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/ Versions/A/CarbonCore 0x90462000 - 0x905c2ff3 libSystem.B.dylib ??? (???) <a12f397abf2285077b89bd726bff5b18> /usr/lib/libSystem.B.dylib 0x90666000 - 0x90666ffa com.apple.CoreServices 32 (32) <2760719f7a81e8c2bdfd15b0939abc29> /System/Library/Frameworks/ CoreServices.framework/Versions/A/CoreServices 0x907ee000 - 0x907f5ffe libbsm.dylib ??? (???) <5582985a86ea36504cca31788bccf963> /usr/lib/libbsm.dylib 0x90941000 - 0x90941ffb com.apple.installserver.framework 1.0 (8) / System/Library/PrivateFrameworks/InstallServer.framework/Versions/A/ InstallServer 0x90993000 - 0x909edff7 com.apple.CoreText 2.0.2 (???) <9fde11f84a72e890bbf2aa8b0b13b79a> /System/Library/Frameworks/ ApplicationServices.framework/Versions/A/Frameworks/CoreText.framework/ Versions/A/CoreText 0x909ee000 - 0x90ec1ffe libGLProgrammability.dylib ??? (???) <475db64244e011cd8811e076035b2632> /System/Library/Frameworks/ OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib 0x911e3000 - 0x911e4ffc libffi.dylib ??? (???) <596e0dbf626b211741cecaa9698f271b> /usr/lib/libffi.dylib 0x911e5000 - 0x91212feb libvDSP.dylib ??? (???) <2ee4eb005babc90eaa352b33eb09226e> /System/Library/Frameworks/ Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/ libvDSP.dylib 0x91213000 - 0x91242fe3 com.apple.AE 402.2 (402.2) <d0da935e781446faa4563e7a9c587cce> /System/Library/Frameworks/ CoreServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE 0x91243000 - 0x91247fff libmathCommon.A.dylib ??? (???) /usr/lib/ system/libmathCommon.A.dylib 0x91248000 - 0x9125efff com.apple.DictionaryServices 1.0.0 (1.0.0) <7e9ff586b5c9d02b09e2a5527d98524f> /System/Library/Frameworks/ CoreServices.framework/Versions/A/Frameworks/ DictionaryServices.framework/Versions/A/DictionaryServices 0x9125f000 - 0x9129efef libTIFF.dylib ??? (???) <4b7d3b3b9a9c8335c2538371cb39b60b> /System/Library/Frameworks/ ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ Versions/A/Resources/libTIFF.dylib 0x9129f000 - 0x912b3ff3 com.apple.ImageCapture 4.0 (5.0.0) /System/ Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ ImageCapture.framework/Versions/A/ImageCapture 0x913ec000 - 0x91426fff com.apple.coreui 1.1 (61) /System/Library/ PrivateFrameworks/CoreUI.framework/Versions/A/CoreUI 0x91427000 - 0x914cefeb com.apple.QD 3.11.52 (???) <d6efc4827b91e646965d15c409a6610f> /System/Library/Frameworks/ ApplicationServices.framework/Versions/A/Frameworks/QD.framework/ Versions/A/QD 0x91b20000 - 0x91b28fff com.apple.DiskArbitration 2.2.1 (2.2.1) <42908e7ecc17a83cec4afef2850ec79e> /System/Library/Frameworks/ DiskArbitration.framework/Versions/A/DiskArbitration 0x91b2f000 - 0x91b5afe7 libauto.dylib ??? (???) <2072d673706bbe463ed2426af57a28d7> /usr/lib/libauto.dylib 0x91b9a000 - 0x91c1cffb com.apple.CFNetwork 330 (330) <6c5eda16e640b09334809ba4c1df985d> /System/Library/Frameworks/ CoreServices.framework/Versions/A/Frameworks/CFNetwork.framework/ Versions/A/CFNetwork 0x91c1d000 - 0x91ce8fff com.apple.ColorSync 4.5.0 (4.5.0) /System/ Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ ColorSync.framework/Versions/A/ColorSync 0x91ce9000 - 0x91d99fff edu.mit.Kerberos 6.0.12 (6.0.12) <1dc515ebe407292db8e603938c72d4e8> /System/Library/Frameworks/ Kerberos.framework/Versions/A/Kerberos 0x91daa000 - 0x91dacfff com.apple.securityhi 3.0 (30817) <020419ad33b8638b174e1a472728a894> /System/Library/Frameworks/ Carbon.framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/ SecurityHI 0x91dad000 - 0x91e06ff7 libGLU.dylib ??? (???) /System/Library/ Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib 0x91e07000 - 0x9219dfff com.apple.QuartzCore 1.5.3 (1.5.3) <1b65c05f89e81a499302fd63295b242d> /System/Library/Frameworks/ QuartzCore.framework/Versions/A/QuartzCore 0x9219e000 - 0x92218ff8 com.apple.print.framework.PrintCore 5.5.3 (245.3) <222dade7b33b99708b8c09d1303f93fc> /System/Library/Frameworks/ ApplicationServices.framework/Versions/A/Frameworks/ PrintCore.framework/Versions/A/PrintCore 0x922ed000 - 0x9230bfff libresolv.9.dylib ??? (???) <32ccbe19e89a3fdd09a0c88151ea508c> /usr/lib/libresolv.9.dylib 0x9230c000 - 0x923edff7 libxml2.2.dylib ??? (???) <1baef3d4972ee789d8fa6c1fa44da45c> /usr/lib/libxml2.2.dylib 0x9250f000 - 0x92babfff com.apple.CoreGraphics 1.351.31 (???) <c97a42498636b2596764e48669f98e00> /System/Library/Frameworks/ ApplicationServices.framework/Versions/A/Frameworks/ CoreGraphics.framework/Versions/A/CoreGraphics 0x92d32000 - 0x92d32ff8 com.apple.ApplicationServices 34 (34) <e9cd7c823062c4382d89e3c9997f4739> /System/Library/Frameworks/ ApplicationServices.framework/Versions/A/ApplicationServices 0x92e82000 - 0x92e8bfff com.apple.speech.recognition.framework 3.7.24 (3.7.24) <6a6518b392d3d41ace3dcea69d6809d9> /System/Library/Frameworks/ Carbon.framework/Versions/A/Frameworks/SpeechRecognition.framework/ Versions/A/SpeechRecognition 0x92e8c000 - 0x92eabffa libJPEG.dylib ??? (???) <c776945af9d960ccf5a80aa2d89fd918> /System/Library/Frameworks/ ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ Versions/A/Resources/libJPEG.dylib 0x92eac000 - 0x92f66fe3 com.apple.CoreServices.OSServices 226.3 (226.3) <456bdd65b936baf1ef497b74b4f960a8> /System/Library/Frameworks/ CoreServices.framework/Versions/A/Frameworks/OSServices.framework/ Versions/A/OSServices 0x93193000 - 0x931a1ffd libz.1.dylib ??? (???) <545ca09467025f77131cfac09d8b9375> /usr/lib/libz.1.dylib 0x932cb000 - 0x93498fe7 com.apple.security 5.0.3 (33532) <3bef414f3c6f433e707ac5abee340e16> /System/Library/Frameworks/ Security.framework/Versions/A/Security 0x93507000 - 0x93592fff com.apple.framework.IOKit 1.5.1 (???) <60cfc4b175c4ef60bb8e9036716a29f4> /System/Library/Frameworks/ IOKit.framework/Versions/A/IOKit 0x93593000 - 0x93610fef libvMisc.dylib ??? (???) /System/Library/ Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/ Versions/A/libvMisc.dylib 0x93611000 - 0x9364fff7 libGLImage.dylib ??? (???) <093b1b698ca93a0380f5fa262459ea28> /System/Library/Frameworks/ OpenGL.framework/Versions/A/Libraries/libGLImage.dylib 0x93650000 - 0x936ccfeb com.apple.audio.CoreAudio 3.1.0 (3.1) <be7120e91df91425e904d5327b4338b7> /System/Library/Frameworks/ CoreAudio.framework/Versions/A/CoreAudio 0x936d2000 - 0x93751ff5 com.apple.SearchKit 1.2.0 (1.2.0) <5abfde5537969168b8a8743ccb9ec735> /System/Library/Frameworks/ CoreServices.framework/Versions/A/Frameworks/SearchKit.framework/ Versions/A/SearchKit 0x9390e000 - 0x9390effd com.apple.Accelerate.vecLib 3.4.2 (vecLib 3.4.2) /System/Library/Frameworks/Accelerate.framework/Versions/A/ Frameworks/vecLib.framework/Versions/A/vecLib 0x9396e000 - 0x939b0fef com.apple.NavigationServices 3.5.2 (163) <91844980804067b07a0b6124310d3f31> /System/Library/Frameworks/ Carbon.framework/Versions/A/Frameworks/NavigationServices.framework/ Versions/A/NavigationServices 0x939b1000 - 0x939b1fff com.apple.Carbon 136 (136) <ec1d4184925e652dbe1b9200a5a552ec> /System/Library/Frameworks/ Carbon.framework/Versions/A/Carbon 0x939b2000 - 0x93a45ff3 com.apple.ApplicationServices.ATS 3.3 (???) <064eb6d96417afa38a80b1735c4113aa> /System/Library/Frameworks/ ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/ Versions/A/ATS 0x93a53000 - 0x93d5aff7 com.apple.HIToolbox 1.5.3 (???) <e36f5c553e5a32f64b7eb458dadadc71> /System/Library/Frameworks/ Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/ HIToolbox 0x93fc4000 - 0x94382fea libLAPACK.dylib ??? (???) /System/Library/ Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/ Versions/A/libLAPACK.dylib 0x943a7000 - 0x944d9fff com.apple.CoreFoundation 6.5.2 (476.13) <b633d15f2901d73670cb1475628df1b3> /System/Library/Frameworks/ CoreFoundation.framework/Versions/A/CoreFoundation 0x944da000 - 0x94502fff libcups.2.dylib ??? (???) <ece20dff2a2c8ed3ae6ef735ef440c37> /usr/lib/libcups.2.dylib 0x94503000 - 0x94553ff7 com.apple.HIServices 1.7.0 (???) <f83f0cb838a646c69f08fd38a31265f3> /System/Library/Frameworks/ ApplicationServices.framework/Versions/A/Frameworks/ HIServices.framework/Versions/A/HIServices 0x94557000 - 0x945b4ffb libstdc++.6.dylib ??? (???) <6106b1f2b0b303b06ae476253dbb5f3f> /usr/lib/libstdc++.6.dylib 0x95666000 - 0x957acff7 com.apple.ImageIO.framework 2.0.2 (2.0.2) <77dfee73f4c0d230425a5151ee0bce05> /System/Library/Frameworks/ ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ Versions/A/ImageIO 0x957ad000 - 0x957afff5 libRadiance.dylib ??? (???) <c307054a6d8337c85ef501780b54704d> /System/Library/Frameworks/ ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ Versions/A/Resources/libRadiance.dylib 0x957b0000 - 0x957c0ffc com.apple.LangAnalysis 1.6.4 (1.6.4) <fc8a73eb3d8b94467d46b81759f65d97> /System/Library/Frameworks/ ApplicationServices.framework/Versions/A/Frameworks/ LangAnalysis.framework/Versions/A/LangAnalysis 0x957c1000 - 0x95873ffb libcrypto.0.9.7.dylib ??? (???) <8f92cbdc8777bea2ec49b06ee79fabc0> /usr/lib/libcrypto.0.9.7.dylib 0x95874000 - 0x959acff7 libicucore.A.dylib ??? (???) <5031226ea28b371d8dfdbb32acfb48b5> /usr/lib/libicucore.A.dylib 0x959d8000 - 0x959f0fff com.apple.openscripting 1.2.6 (???) <4e0b05f9f47c6f7e2b01b321b2eb1413> /System/Library/Frameworks/ Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/ Versions/A/OpenScripting 0x959f1000 - 0x95e01fef libBLAS.dylib ??? (???) /System/Library/ Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/ Versions/A/libBLAS.dylib 0x95e02000 - 0x95e5eff7 com.apple.htmlrendering 68 (1.1.3) <a9f65fa1c4668dc7c49af5bf7d5287ad> /System/Library/Frameworks/ Carbon.framework/Versions/A/Frameworks/HTMLRendering.framework/ Versions/A/HTMLRendering 0x95eaf000 - 0x95eb5fff com.apple.print.framework.Print 218.0.2 (220.1) <2979f3be4e7e8adc875bf21658e9be94> /System/Library/Frameworks/ Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/Print 0x966b4000 - 0x9673bff7 libsqlite3.0.dylib ??? (???) <11311084bc4be9d4555dfac74fe7218a> /usr/lib/libsqlite3.0.dylib 0x9679e000 - 0x9687dfff libobjc.A.dylib ??? (???) <99a9ad33ca07114848fdd7580968a572> /usr/lib/libobjc.A.dylib 0x96994000 - 0x969b8fff libxslt.1.dylib ??? (???) <59399cc446ed903fd9479526ee9f116b> /usr/lib/libxslt.1.dylib 0x969b9000 - 0x969bdfff libGIF.dylib ??? (???) <75b4fd9684d792add088205f987fb02e> /System/Library/Frameworks/ ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ Versions/A/Resources/libGIF.dylib 0x969fc000 - 0x96c77fe7 com.apple.Foundation 6.5.5 (677.19) <bfd4ebea1a7739dd6b523f15dca01a37> /System/Library/Frameworks/ Foundation.framework/Versions/C/Foundation 0x96cbf000 - 0x96ccbfe7 com.apple.opengl 1.5.6 (1.5.6) <125de77ea2434a91364e79a0905a7771> /System/Library/Frameworks/ OpenGL.framework/Versions/A/OpenGL 0x96d03000 - 0x96d8fff7 com.apple.LaunchServices 289.2 (289.2) <3577886e3a6d56ee3949850c4fde76c9> /System/Library/Frameworks/ CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/ Versions/A/LaunchServices 0x96d90000 - 0x96d93fff com.apple.help 1.1 (36) <175489f8adf287b3ebd259362b0292c0> /System/Library/Frameworks/ Carbon.framework/Versions/A/Frameworks/Help.framework/Versions/A/Help 0x96d94000 - 0x96db4ff2 libGL.dylib ??? (???) /System/Library/ Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib 0x96db5000 - 0x96e48fff com.apple.ink.framework 101.3 (86) <dfa9debcd7537849d228021d1d9c0f63> /System/Library/Frameworks/ Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink 0x96f3e000 - 0x96fc8fe3 com.apple.DesktopServices 1.4.6 (1.4.6) <94d1a28b351b7dff77becadab0967772> /System/Library/PrivateFrameworks/ DesktopServicesPriv.framework/Versions/A/DesktopServicesPriv 0x96fc9000 - 0x96fd0fe9 libgcc_s.1.dylib ??? (???) <28a7cbc3a5ca2982d124668306f422d9> /usr/lib/libgcc_s.1.dylib 0x96fd1000 - 0x96fdbfeb com.apple.audio.SoundManager 3.9.2 (3.9.2) <caa41909dcb5a18a94bc68cd13999bd5> /System/Library/Frameworks/ Carbon.framework/Versions/A/Frameworks/CarbonSound.framework/Versions/ A/CarbonSound 0x96fdd000 - 0x96fedfff com.apple.speech.synthesis.framework 3.7.1 (3.7.1) <06d8fc0307314f8ffc16f206ad3dbf44> /System/Library/Frameworks/ ApplicationServices.framework/Versions/A/Frameworks/ SpeechSynthesis.framework/Versions/A/SpeechSynthesis 0x97055000 - 0x9711cff2 com.apple.vImage 3.0 (3.0) /System/Library/ Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/ Versions/A/vImage 0x9711d000 - 0x9711dffd com.apple.Accelerate 1.4.2 (Accelerate 1.4.2) /System/Library/Frameworks/Accelerate.framework/Versions/A/ Accelerate 0x9715e000 - 0x97179ff3 libPng.dylib ??? (???) <c0484bec6e2432b406755591924fe664> /System/Library/Frameworks/ ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ Versions/A/Resources/libPng.dylib 0x9717a000 - 0x971c0fef com.apple.Metadata 10.5.2 (398.18) <adbb3a14e8f7da444e16d2fd61862771> /System/Library/Frameworks/ CoreServices.framework/Versions/A/Frameworks/Metadata.framework/ Versions/A/Metadata 0x971f6000 - 0x971fbfff com.apple.CommonPanels 1.2.4 (85) <3b64ef0de184d09c6f99a1a7e77e42be> /System/Library/Frameworks/ Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/Versions/ A/CommonPanels 0x971fc000 - 0x97233fff com.apple.SystemConfiguration 1.9.2 (1.9.2) <8b26ebf26a009a098484f1ed01ec499c> /System/Library/Frameworks/ SystemConfiguration.framework/Versions/A/SystemConfiguration 0xfffe8000 - 0xfffebfff libobjc.A.dylib ??? (???) /usr/lib/ libobjc.A.dylib 0xffff0000 - 0xffff1780 libSystem.B.dylib ??? (???) /usr/lib/ libSystem.B.dylib -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 0 15 77 - 1 90 31 41 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

2 2

2D images
by jewet037＠umn.edu 18 Jun '08

18 Jun '08

Hi, I would like to create a properly proportioned 2-dimensional map of hemispheric surfaces to use for displaying average vertex values within parcellated regions or individual values for each vertex. At the moment, we can access the matrix of vertex values (i.e. the scalars computed at each vertex of the equilateral triangles along the surface), but we don't know how to associate these values with the regions they came from, or how to plot them on a 2D surface. Thanks, Ethan

2 1

FreeSurfer tksurfer
by Pedro Brito Cruz 18 Jun '08

18 Jun '08

Dear all, i'm a newbie using FreeSurfer and recently installed the CentOS 4 x86_64 version on my 64 bit processor with Linux Ubuntu (dapper version). I followed the tutorial for testing the installation and tkmedit tool worked fine but tksurfer did not. I got the following error, tksurfer bert rh pial surfer: current subjects dir: $FREESURFER_HOME/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: Reading header info from $FREESURFER_HOME/subjects/bert/mri/T1.mgz surfer: vertices=131168, faces=262332 Received X error! Error code : 163 Request code : 148 Minor code : 2 Error text : 'GLXBadLargeRequest' Does anybody know what can i do to solve this problemL? Thanks in advance. Pedro

2 1

ICV accuracy
by Jared Conley 18 Jun '08

18 Jun '08

FreeSurfer Community: A quick question for the group. Our lab was wondering if there is an easy way to assess the accuracy of the intracranial volume (ICV) measurement? Or is this not necessary (never any errors)? Thanks in advance, Jared -- Jared Conley Center for Neurological Imaging Brigham and Women's Hospital Harvard Medical School 221 Longwood Ave., RF 394 P: 617.525.6238

2 2

Re: Further questions regarding freesurfer 4.0.5
by Liat Levita 18 Jun '08

18 Jun '08

Hi all, we are also having some problems with v4.05 (Mac computer PC Tiger) -we keep getting problems with edit segmentation All seems well until we perform the following sequance of actions: 1. Press mouse button 3 to erase voxels from a particular ROI. 2. Press mouse button 2 to add voxels to a selected ROI (after having chosen the appropriate label in 'Configure Segmentation Brush' tool option. 3. Then press mouse button 3 to erase voxels (from any region not necessarily what we have just been working on) - Now instead of just erasing it adds the label 'nerve' to area that we want to delete. We have tried playing around with this, and have now gone back to our older version of freesurfer where this doesn't happen. We also get the following error message while doing 'Edit Segmentation' which causes the system to crash. ErrorLog: --------- syntax error in expression " * 2": unexpected operator * syntax error in expression " * 2": unexpected operator * while executing "expr $nSelection * 2" (procedure "SendSegBrushInfo" line 11) invoked from within "SendSegBrushInfo" invoked from within ".wwEditSegBrushInfoDlog.lfwFill.border.frame.fwFill.fwSegSrc.rbw invoke" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w $cmd]" (procedure "tk::CheckRadioInvoke" line 3) invoked from within "tk::CheckRadioInvoke .wwEditSegBrushInfoDlog.lfwFill.border.frame.fwFill.fwSegSrc.rbw" (command bound to event) *** *** *** *** *** Liat Levita, PhD Instructor of Psychology in Psychiatry Sackler Institute for Developmental Psychobiology Weill Medical College of Cornell University 1300 York Ave, Box 140 New York, NY 10021 Tel: 212 746 5836 Fax: 212 746 5755 http://www.sacklerinstitute.org/cornell ----- Original Message ----- From: Sebastian Moeller <sebastian.moeller(a)lur.rwth-aachen.de> Date: Wednesday, June 18, 2008 4:57 am Subject: [Freesurfer] questions regarding freesurfer 4.0.5 > First, if this shows up twice, let m apologise for mixing up my > email > addresses... > > Aloha fellow surfers, > > > I just installed > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Darwin-leopard- > i686-stable-pub-v4.0.5-full.dmg > on my: > intel macbook, running 10.5.3 with 4GB of RAM. A few observations: > 1) minor: freeview does not seem to be part of the dmg, probably > expected, but from the release notes it is not obvious, whether the > > macos version should contain it or not > 2) minor, minor: it seems like the whole macos version is built for > > 32bit only (at least that is what "file `which mri_convert`" and a > few > other binaries tell me); would it be possible to have a 64bit built > > (than my macbook might suffice for surface reconstruction as well). > > 3) scuba dies horribly (tkmedit and tksurfer, however seem to work, > at > least they start up and display something), here is the problem > report: > Path: /opt/freesurfer//bin/scuba.bin > Identifier: scuba.bin > Version: ??? (???) > Code Type: X86 (Native) > Parent Process: tcsh [18243] > > Date/Time: 2008-06-18 10:10:42.832 +0200 > OS Version: Mac OS X 10.5.3 (9D34) > Report Version: 6 > > Exception Type: EXC_BAD_ACCESS (SIGBUS) > Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000000000000 > Crashed Thread: 0 > > Thread 0 Crashed: > 0 scuba.bin 0x001e5764 0x1000 + 1984356 > 1 dyld 0x8fe0e723 > ImageLoader::recursiveInitialization(ImageLoader::LinkContext > const&, > unsigned int) + 307 > 2 dyld 0x8fe0e809 > ImageLoader::runInitializers(ImageLoader::LinkContext const&) + 57 > 3 dyld 0x8fe04102 > dyld::initializeMainExecutable() + 146 > 4 dyld 0x8fe07b5f > dyld::_main(mach_header > const*, unsigned long, int, char const**, char const**, char > const**) > + 2975 > 5 dyld 0x8fe01872 > dyldbootstrap::start(mach_header const*, int, char const**, long) + > 8186 dyld 0x8fe01037 _dyld_start + 39 > > Thread 0 crashed with X86 Thread State (32-bit): > eax: 0x00000000 ebx: 0x001e570c ecx: 0x00000002 edx: 0x00000000 > edi: 0x00000026 esi: 0x00001000 ebp: 0xbfffd548 esp: 0xbfffd4c0 > ss: 0x0000001f efl: 0x00010282 eip: 0x001e5764 cs: 0x00000017 > ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037 > cr2: 0x00000000 > > Binary Images: > 0x1000 - 0x23ffed +scuba.bin ??? (???) > <d06ab65353013407522c78a886efea54> /opt/freesurfer/bin/scuba.bin > 0x2af000 - 0x35ffe9 +libGLU.1.dylib ??? (???) > /usr/X11/lib/libGLU. > 1.dylib > 0x37a000 - 0x38efe7 +libXmu.6.dylib ??? (???) > <4368a7afa86da654c52e64ba19a9097b> /usr/X11/lib/libXmu.6.dylib > 0x397000 - 0x3e2ff8 +libXt.6.dylib ??? (???) > <d700ce75d38c60146177b10c3883f10d> /usr/X11/lib/libXt.6.dylib > 0x3f7000 - 0x3fcffc +libSM.6.dylib ??? (???) > <1a5a19fa53bdce9d344782a05db3c4e7> /usr/X11/lib/libSM.6.dylib > 0x402000 - 0x413ff7 +libICE.6.dylib ??? (???) > <0ed3bdd6f53b07a00ef27fc3577f283a> /usr/X11/lib/libICE.6.dylib > 0x41c000 - 0x428ffa +libXext.6.dylib ??? (???) > <a94a1adf7793da948691b99b4777e2e1> /usr/X11/lib/libXext.6.dylib > 0x430000 - 0x51bfe7 +libX11.6.dylib ??? (???) > <cc5a62e8982326ffe327eafb901129d3> /usr/X11/lib/libX11.6.dylib > 0x53d000 - 0x53ffef +libXdmcp.6.dylib ??? (???) > <6f2b16b27bab3a08bd635d8e56bfe9f6> /usr/X11/lib/libXdmcp.6.dylib > 0x544000 - 0x544ff1 +libXau.6.dylib ??? (???) > <cd091bf5ae82c18ee03a9b4f6bb93d57> /usr/X11/lib/libXau.6.dylib > 0x549000 - 0x596fe7 +libGL.1.dylib ??? (???) > <f96baeea46fa05910212d7427da5f33a> /usr/X11/lib/libGL.1.dylib > 0x5c3000 - 0x5cefeb libXplugin.1.dylib ??? (???) > <b175d293d67060cbf50aa111b2ab41b0> /usr/lib/libXplugin.1.dylib > 0x5d7000 - 0x5edfe7 com.apple.CoreVideo 1.5.1 (1.5.1) > <ed7bb95fb94817ea3212090aac5c65f3> /System/Library/Frameworks/ > CoreVideo.framework/Versions/A/CoreVideo > 0xa000000 - 0xa07cfef +libtcl8.4.dylib ??? (???) > /opt/freesurfer/lib/ > tcltktixblt/lib/libtcl8.4.dylib > 0xb000000 - 0xb0a4fff +libtk8.4.dylib ??? (???) > <09a6ab5749f362ad8838bfe610a8f33f> > /opt/freesurfer/lib/tcltktixblt/lib/ > libtk8.4.dylib > 0x8fe00000 - 0x8fe2da53 dyld 96.2 (???) > <5013f43c4d2c33c9619011f103ec3238> /usr/lib/dyld > 0x90003000 - 0x902ddff3 com.apple.CoreServices.CarbonCore 786.4 > (786.4) <059c4803a7a95e3c1a95a332baeb1edf> > /System/Library/Frameworks/ > CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/ > Versions/A/CarbonCore > 0x90462000 - 0x905c2ff3 libSystem.B.dylib ??? (???) > <a12f397abf2285077b89bd726bff5b18> /usr/lib/libSystem.B.dylib > 0x90666000 - 0x90666ffa com.apple.CoreServices 32 (32) > <2760719f7a81e8c2bdfd15b0939abc29> /System/Library/Frameworks/ > CoreServices.framework/Versions/A/CoreServices > 0x907ee000 - 0x907f5ffe libbsm.dylib ??? (???) > <5582985a86ea36504cca31788bccf963> /usr/lib/libbsm.dylib > 0x90941000 - 0x90941ffb com.apple.installserver.framework 1.0 (8) > / > System/Library/PrivateFrameworks/InstallServer.framework/Versions/A/ > InstallServer > 0x90993000 - 0x909edff7 com.apple.CoreText 2.0.2 (???) > <9fde11f84a72e890bbf2aa8b0b13b79a> /System/Library/Frameworks/ > ApplicationServices.framework/Versions/A/Frameworks/CoreText.framework/ > Versions/A/CoreText > 0x909ee000 - 0x90ec1ffe libGLProgrammability.dylib ??? (???) > <475db64244e011cd8811e076035b2632> /System/Library/Frameworks/ > OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib > 0x911e3000 - 0x911e4ffc libffi.dylib ??? (???) > <596e0dbf626b211741cecaa9698f271b> /usr/lib/libffi.dylib > 0x911e5000 - 0x91212feb libvDSP.dylib ??? (???) > <2ee4eb005babc90eaa352b33eb09226e> /System/Library/Frameworks/ > Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/ > libvDSP.dylib > 0x91213000 - 0x91242fe3 com.apple.AE 402.2 (402.2) > <d0da935e781446faa4563e7a9c587cce> /System/Library/Frameworks/ > CoreServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE > 0x91243000 - 0x91247fff libmathCommon.A.dylib ??? (???) /usr/lib/ > system/libmathCommon.A.dylib > 0x91248000 - 0x9125efff com.apple.DictionaryServices 1.0.0 (1.0.0) > > <7e9ff586b5c9d02b09e2a5527d98524f> /System/Library/Frameworks/ > CoreServices.framework/Versions/A/Frameworks/ > DictionaryServices.framework/Versions/A/DictionaryServices > 0x9125f000 - 0x9129efef libTIFF.dylib ??? (???) > <4b7d3b3b9a9c8335c2538371cb39b60b> /System/Library/Frameworks/ > ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ > Versions/A/Resources/libTIFF.dylib > 0x9129f000 - 0x912b3ff3 com.apple.ImageCapture 4.0 (5.0.0) > /System/ > Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ > ImageCapture.framework/Versions/A/ImageCapture > 0x913ec000 - 0x91426fff com.apple.coreui 1.1 (61) /System/Library/ > PrivateFrameworks/CoreUI.framework/Versions/A/CoreUI > 0x91427000 - 0x914cefeb com.apple.QD 3.11.52 (???) > <d6efc4827b91e646965d15c409a6610f> /System/Library/Frameworks/ > ApplicationServices.framework/Versions/A/Frameworks/QD.framework/ > Versions/A/QD > 0x91b20000 - 0x91b28fff com.apple.DiskArbitration 2.2.1 (2.2.1) > <42908e7ecc17a83cec4afef2850ec79e> /System/Library/Frameworks/ > DiskArbitration.framework/Versions/A/DiskArbitration > 0x91b2f000 - 0x91b5afe7 libauto.dylib ??? (???) > <2072d673706bbe463ed2426af57a28d7> /usr/lib/libauto.dylib > 0x91b9a000 - 0x91c1cffb com.apple.CFNetwork 330 (330) > <6c5eda16e640b09334809ba4c1df985d> /System/Library/Frameworks/ > CoreServices.framework/Versions/A/Frameworks/CFNetwork.framework/ > Versions/A/CFNetwork > 0x91c1d000 - 0x91ce8fff com.apple.ColorSync 4.5.0 (4.5.0) /System/ > Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ > ColorSync.framework/Versions/A/ColorSync > 0x91ce9000 - 0x91d99fff edu.mit.Kerberos 6.0.12 (6.0.12) > <1dc515ebe407292db8e603938c72d4e8> /System/Library/Frameworks/ > Kerberos.framework/Versions/A/Kerberos > 0x91daa000 - 0x91dacfff com.apple.securityhi 3.0 (30817) > <020419ad33b8638b174e1a472728a894> /System/Library/Frameworks/ > Carbon.framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/ > SecurityHI > 0x91dad000 - 0x91e06ff7 libGLU.dylib ??? (???) /System/Library/ > Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib > 0x91e07000 - 0x9219dfff com.apple.QuartzCore 1.5.3 (1.5.3) > <1b65c05f89e81a499302fd63295b242d> /System/Library/Frameworks/ > QuartzCore.framework/Versions/A/QuartzCore > 0x9219e000 - 0x92218ff8 com.apple.print.framework.PrintCore 5.5.3 > (245.3) <222dade7b33b99708b8c09d1303f93fc> > /System/Library/Frameworks/ > ApplicationServices.framework/Versions/A/Frameworks/ > PrintCore.framework/Versions/A/PrintCore > 0x922ed000 - 0x9230bfff libresolv.9.dylib ??? (???) > <32ccbe19e89a3fdd09a0c88151ea508c> /usr/lib/libresolv.9.dylib > 0x9230c000 - 0x923edff7 libxml2.2.dylib ??? (???) > <1baef3d4972ee789d8fa6c1fa44da45c> /usr/lib/libxml2.2.dylib > 0x9250f000 - 0x92babfff com.apple.CoreGraphics 1.351.31 (???) > <c97a42498636b2596764e48669f98e00> /System/Library/Frameworks/ > ApplicationServices.framework/Versions/A/Frameworks/ > CoreGraphics.framework/Versions/A/CoreGraphics > 0x92d32000 - 0x92d32ff8 com.apple.ApplicationServices 34 (34) > <e9cd7c823062c4382d89e3c9997f4739> /System/Library/Frameworks/ > ApplicationServices.framework/Versions/A/ApplicationServices > 0x92e82000 - 0x92e8bfff com.apple.speech.recognition.framework > 3.7.24 > (3.7.24) <6a6518b392d3d41ace3dcea69d6809d9> > /System/Library/Frameworks/ > Carbon.framework/Versions/A/Frameworks/SpeechRecognition.framework/ > Versions/A/SpeechRecognition > 0x92e8c000 - 0x92eabffa libJPEG.dylib ??? (???) > <c776945af9d960ccf5a80aa2d89fd918> /System/Library/Frameworks/ > ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ > Versions/A/Resources/libJPEG.dylib > 0x92eac000 - 0x92f66fe3 com.apple.CoreServices.OSServices 226.3 > (226.3) <456bdd65b936baf1ef497b74b4f960a8> > /System/Library/Frameworks/ > CoreServices.framework/Versions/A/Frameworks/OSServices.framework/ > Versions/A/OSServices > 0x93193000 - 0x931a1ffd libz.1.dylib ??? (???) > <545ca09467025f77131cfac09d8b9375> /usr/lib/libz.1.dylib > 0x932cb000 - 0x93498fe7 com.apple.security 5.0.3 (33532) > <3bef414f3c6f433e707ac5abee340e16> /System/Library/Frameworks/ > Security.framework/Versions/A/Security > 0x93507000 - 0x93592fff com.apple.framework.IOKit 1.5.1 (???) > <60cfc4b175c4ef60bb8e9036716a29f4> /System/Library/Frameworks/ > IOKit.framework/Versions/A/IOKit > 0x93593000 - 0x93610fef libvMisc.dylib ??? (???) /System/Library/ > Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/ > Versions/A/libvMisc.dylib > 0x93611000 - 0x9364fff7 libGLImage.dylib ??? (???) > <093b1b698ca93a0380f5fa262459ea28> /System/Library/Frameworks/ > OpenGL.framework/Versions/A/Libraries/libGLImage.dylib > 0x93650000 - 0x936ccfeb com.apple.audio.CoreAudio 3.1.0 (3.1) > <be7120e91df91425e904d5327b4338b7> /System/Library/Frameworks/ > CoreAudio.framework/Versions/A/CoreAudio > 0x936d2000 - 0x93751ff5 com.apple.SearchKit 1.2.0 (1.2.0) > <5abfde5537969168b8a8743ccb9ec735> /System/Library/Frameworks/ > CoreServices.framework/Versions/A/Frameworks/SearchKit.framework/ > Versions/A/SearchKit > 0x9390e000 - 0x9390effd com.apple.Accelerate.vecLib 3.4.2 (vecLib > 3.4.2) /System/Library/Frameworks/Accelerate.framework/Versions/A/ > Frameworks/vecLib.framework/Versions/A/vecLib > 0x9396e000 - 0x939b0fef com.apple.NavigationServices 3.5.2 (163) > <91844980804067b07a0b6124310d3f31> /System/Library/Frameworks/ > Carbon.framework/Versions/A/Frameworks/NavigationServices.framework/ > Versions/A/NavigationServices > 0x939b1000 - 0x939b1fff com.apple.Carbon 136 (136) > <ec1d4184925e652dbe1b9200a5a552ec> /System/Library/Frameworks/ > Carbon.framework/Versions/A/Carbon > 0x939b2000 - 0x93a45ff3 com.apple.ApplicationServices.ATS 3.3 > (???) > <064eb6d96417afa38a80b1735c4113aa> /System/Library/Frameworks/ > ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/ > Versions/A/ATS > 0x93a53000 - 0x93d5aff7 com.apple.HIToolbox 1.5.3 (???) > <e36f5c553e5a32f64b7eb458dadadc71> /System/Library/Frameworks/ > Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/ > HIToolbox > 0x93fc4000 - 0x94382fea libLAPACK.dylib ??? (???) /System/Library/ > Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/ > Versions/A/libLAPACK.dylib > 0x943a7000 - 0x944d9fff com.apple.CoreFoundation 6.5.2 (476.13) > <b633d15f2901d73670cb1475628df1b3> /System/Library/Frameworks/ > CoreFoundation.framework/Versions/A/CoreFoundation > 0x944da000 - 0x94502fff libcups.2.dylib ??? (???) > <ece20dff2a2c8ed3ae6ef735ef440c37> /usr/lib/libcups.2.dylib > 0x94503000 - 0x94553ff7 com.apple.HIServices 1.7.0 (???) > <f83f0cb838a646c69f08fd38a31265f3> /System/Library/Frameworks/ > ApplicationServices.framework/Versions/A/Frameworks/ > HIServices.framework/Versions/A/HIServices > 0x94557000 - 0x945b4ffb libstdc++.6.dylib ??? (???) > <6106b1f2b0b303b06ae476253dbb5f3f> /usr/lib/libstdc++.6.dylib > 0x95666000 - 0x957acff7 com.apple.ImageIO.framework 2.0.2 (2.0.2) > <77dfee73f4c0d230425a5151ee0bce05> /System/Library/Frameworks/ > ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ > Versions/A/ImageIO > 0x957ad000 - 0x957afff5 libRadiance.dylib ??? (???) > <c307054a6d8337c85ef501780b54704d> /System/Library/Frameworks/ > ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ > Versions/A/Resources/libRadiance.dylib > 0x957b0000 - 0x957c0ffc com.apple.LangAnalysis 1.6.4 (1.6.4) > <fc8a73eb3d8b94467d46b81759f65d97> /System/Library/Frameworks/ > ApplicationServices.framework/Versions/A/Frameworks/ > LangAnalysis.framework/Versions/A/LangAnalysis > 0x957c1000 - 0x95873ffb libcrypto.0.9.7.dylib ??? (???) > <8f92cbdc8777bea2ec49b06ee79fabc0> /usr/lib/libcrypto.0.9.7.dylib > 0x95874000 - 0x959acff7 libicucore.A.dylib ??? (???) > <5031226ea28b371d8dfdbb32acfb48b5> /usr/lib/libicucore.A.dylib > 0x959d8000 - 0x959f0fff com.apple.openscripting 1.2.6 (???) > <4e0b05f9f47c6f7e2b01b321b2eb1413> /System/Library/Frameworks/ > Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/ > Versions/A/OpenScripting > 0x959f1000 - 0x95e01fef libBLAS.dylib ??? (???) /System/Library/ > Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/ > Versions/A/libBLAS.dylib > 0x95e02000 - 0x95e5eff7 com.apple.htmlrendering 68 (1.1.3) > <a9f65fa1c4668dc7c49af5bf7d5287ad> /System/Library/Frameworks/ > Carbon.framework/Versions/A/Frameworks/HTMLRendering.framework/ > Versions/A/HTMLRendering > 0x95eaf000 - 0x95eb5fff com.apple.print.framework.Print 218.0.2 > (220.1) <2979f3be4e7e8adc875bf21658e9be94> > /System/Library/Frameworks/ > Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/Print > 0x966b4000 - 0x9673bff7 libsqlite3.0.dylib ??? (???) > <11311084bc4be9d4555dfac74fe7218a> /usr/lib/libsqlite3.0.dylib > 0x9679e000 - 0x9687dfff libobjc.A.dylib ??? (???) > <99a9ad33ca07114848fdd7580968a572> /usr/lib/libobjc.A.dylib > 0x96994000 - 0x969b8fff libxslt.1.dylib ??? (???) > <59399cc446ed903fd9479526ee9f116b> /usr/lib/libxslt.1.dylib > 0x969b9000 - 0x969bdfff libGIF.dylib ??? (???) > <75b4fd9684d792add088205f987fb02e> /System/Library/Frameworks/ > ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ > Versions/A/Resources/libGIF.dylib > 0x969fc000 - 0x96c77fe7 com.apple.Foundation 6.5.5 (677.19) > <bfd4ebea1a7739dd6b523f15dca01a37> /System/Library/Frameworks/ > Foundation.framework/Versions/C/Foundation > 0x96cbf000 - 0x96ccbfe7 com.apple.opengl 1.5.6 (1.5.6) > <125de77ea2434a91364e79a0905a7771> /System/Library/Frameworks/ > OpenGL.framework/Versions/A/OpenGL > 0x96d03000 - 0x96d8fff7 com.apple.LaunchServices 289.2 (289.2) > <3577886e3a6d56ee3949850c4fde76c9> /System/Library/Frameworks/ > CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/ > Versions/A/LaunchServices > 0x96d90000 - 0x96d93fff com.apple.help 1.1 (36) > <175489f8adf287b3ebd259362b0292c0> /System/Library/Frameworks/ > Carbon.framework/Versions/A/Frameworks/Help.framework/Versions/A/Help > 0x96d94000 - 0x96db4ff2 libGL.dylib ??? (???) /System/Library/ > Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib > 0x96db5000 - 0x96e48fff com.apple.ink.framework 101.3 (86) > <dfa9debcd7537849d228021d1d9c0f63> /System/Library/Frameworks/ > Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink > 0x96f3e000 - 0x96fc8fe3 com.apple.DesktopServices 1.4.6 (1.4.6) > <94d1a28b351b7dff77becadab0967772> > /System/Library/PrivateFrameworks/ > DesktopServicesPriv.framework/Versions/A/DesktopServicesPriv > 0x96fc9000 - 0x96fd0fe9 libgcc_s.1.dylib ??? (???) > <28a7cbc3a5ca2982d124668306f422d9> /usr/lib/libgcc_s.1.dylib > 0x96fd1000 - 0x96fdbfeb com.apple.audio.SoundManager 3.9.2 (3.9.2) > > <caa41909dcb5a18a94bc68cd13999bd5> /System/Library/Frameworks/ > Carbon.framework/Versions/A/Frameworks/CarbonSound.framework/Versions/ > A/CarbonSound > 0x96fdd000 - 0x96fedfff com.apple.speech.synthesis.framework 3.7.1 > > (3.7.1) <06d8fc0307314f8ffc16f206ad3dbf44> > /System/Library/Frameworks/ > ApplicationServices.framework/Versions/A/Frameworks/ > SpeechSynthesis.framework/Versions/A/SpeechSynthesis > 0x97055000 - 0x9711cff2 com.apple.vImage 3.0 (3.0) > /System/Library/ > Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/ > Versions/A/vImage > 0x9711d000 - 0x9711dffd com.apple.Accelerate 1.4.2 (Accelerate > 1.4.2) /System/Library/Frameworks/Accelerate.framework/Versions/A/ > Accelerate > 0x9715e000 - 0x97179ff3 libPng.dylib ??? (???) > <c0484bec6e2432b406755591924fe664> /System/Library/Frameworks/ > ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ > Versions/A/Resources/libPng.dylib > 0x9717a000 - 0x971c0fef com.apple.Metadata 10.5.2 (398.18) > <adbb3a14e8f7da444e16d2fd61862771> /System/Library/Frameworks/ > CoreServices.framework/Versions/A/Frameworks/Metadata.framework/ > Versions/A/Metadata > 0x971f6000 - 0x971fbfff com.apple.CommonPanels 1.2.4 (85) > <3b64ef0de184d09c6f99a1a7e77e42be> /System/Library/Frameworks/ > Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/Versions/ > A/CommonPanels > 0x971fc000 - 0x97233fff com.apple.SystemConfiguration 1.9.2 > (1.9.2) > <8b26ebf26a009a098484f1ed01ec499c> /System/Library/Frameworks/ > SystemConfiguration.framework/Versions/A/SystemConfiguration > 0xfffe8000 - 0xfffebfff libobjc.A.dylib ??? (???) /usr/lib/ > libobjc.A.dylib > 0xffff0000 - 0xffff1780 libSystem.B.dylib ??? (???) /usr/lib/ > libSystem.B.dylib > > -- > Sebastian Moeller > > Tel.: 04 21 - 2 18 - 78 38 oder 96 91 > Fax.: 04 21 - 2 18 - 90 04 > GSM: 0 15 77 - 1 90 31 41 > moeller(a)brain.uni-bremen.de > > AG Kreiter / FB 2 > Institut fuer Hirnforschung III > Abteilung Theoretische Neurobiologie > Universitaet Bremen > Biogarten > Hochschulring 16a > Postfach 33 04 40 > 28359 Bremen > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

1 0

X11 - FreeSurfer hot-key problem Mac
by Liat Levita 17 Jun '08

17 Jun '08

Hello, I wonder if anyone else has had this problem on the Mac. I have now installed FreeSurfer (Tiger V4.0.5) on 3 machines, everytime I do this some of my shortcut X11 keys stop working. We are running - X11 1.1.3 - on a Mac OS X 10.4.11 I would really appricate your help with this - Does anyone know how one may fix this. Thank you Liat ----- Original Message ----- From: Krish Subramaniam <krish(a)nmr.mgh.harvard.edu> Date: Tuesday, June 17, 2008 12:54 pm Subject: Re: [Freesurfer] tkmedit --> tksurfer (tkmedit points not being saved) > Aaron and Bruce, > > Looks like tkmedit saves edit.dat in the directory from which it is > > invoked, but tksurfer tries to load edit.dat from the tmp/edit.dat > in > the subject dir. > > A simple workaround is to setenv a variable called > FS_SAVE_GOTO_POINT > to a filename where you want both tkmedit and tksurfer to read/save > > the points. Like, > > setenv FS_SAVE_GOTO_POINT <subject_dir>/tmp/point.dat > > This should work. > > Anyway, tkmedit should try and save the point to the standard > ( documented ) location <subject_dir>/tmp/edit.dat and if it can't > it > should save it to the ./edit.dat... will try and fix this. > > Best, > Krish > > On Jun 16, 2008, at 8:35 PM, Bruce Fischl wrote: > > > the points are stored in the subject's tmp/edit.dat dir. Does > that > > file exist? Is there any error in either of the terminal windows? > > > > On Mon, 16 Jun 2008, Aaron Shmookler wrote: > > > >> Although new to Freesurfer, I have in the past been able to save > > >> points on > >> tkmedit and bring them up on an inflated tksurfer image. > However, > >> now this > >> is not happening. When I click on Save Point or go to > Tools>Save > >> Point in > >> tkmedit, no coordinates are brought up in the tkmedit Terminal > >> window. So, > >> when I try to bring up points on tksurfer (goto saved point) no > >> points are > >> shown. > >> > >> Help would be greatly appreciated. > >> > >> Thanks, > >> Aaron > >> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

1 0

tkmedit --> tksurfer (tkmedit points not being saved)
by Aaron Shmookler 17 Jun '08

17 Jun '08

Although new to Freesurfer, I have in the past been able to save points on tkmedit and bring them up on an inflated tksurfer image. However, now this is not happening. When I click on Save Point or go to Tools>Save Point in tkmedit, no coordinates are brought up in the tkmedit Terminal window. So, when I try to bring up points on tksurfer (goto saved point) no points are shown. Help would be greatly appreciated. Thanks, Aaron

3 2

Qdec error
by Ming Hsu 16 Jun '08

16 Jun '08

Hi, I am getting a qdec error on FreeSurfer 4.0.2 on Tiger. The error has been mentioned on the forum before. In particular qdec.bin seems to be calling for tcl/tk libs in /usr/pubsw which doesn't exist. Below are the first two lines from the ldd profile for qdec.bin. > ldd /Applications/freesurfer/bin/qdec.bin /usr/pubsw/packages/tcltktixblt/current/lib/libtk8.4.dylib (compatibility version 8.4.0, current version 8.4.0) /usr/pubsw/packages/tcltktixblt/current/lib/libtcl8.4.dylib (compatibility version 8.4.0, current version 8.4.0) I tried creating the folder structure and symlink the libraries to the appropriate ones in the Freesurfer distribution, but still got the same error. I saw a suggestion to upgrade to v. 4.0.3, but 4.0.2 is the latest for Tiger on Intel. There is a 4.0.4 for Tiger PPC though. Is it possible to distribute the new version on Intel Tiger? Thanks, Ming -- Ming Hsu Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana, IL 61801 (217) 244-1122 Office

2 3

Re: [Freesurfer] Prob:Software Download Tiger version \
by Liat Levita 16 Jun '08

16 Jun '08

Hi Nick, when it starts downloading you can see it as tiger - but when it finally uploads the package is labeled -freesurfer-Darwin-leopard-full.pkg, which seems very odd. L p.s. I will try wget. Just need to install it on my machine. ----- Original Message ----- From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> Date: Monday, June 16, 2008 12:09 pm Subject: Re: [Freesurfer] Prob:Software Download Tiger version \ > Liat, > > I am unable to recreate what you are seeing. When I click on the > 'freesurfer-Darwin-tiger-ppc-stable-pub-v4.0.5-full.dmg' link > (albeit on > a Linux machine), it downloads that filename. > > You could try: > > wget > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Darwin-tiger- > ppc-stable-pub-v4.0.5-full.dmg > > from a terminal as an alternative. > > Nick > > > On Mon, 2008-06-16 at 11:25 -0400, Liat Levita wrote: > > Hi, I am trying to download the updated FreeSurfer - Mac OS X > Tiger (10.4.11) PowerPC stable v4.0.5 15 June 2008 - freesurfer- > Darwin-tiger-ppc-stable-pub-v4.0.5-full.dmg > > > > However, when I do so I keep getting the zipped Leopard package. > I wonder if something is wrong with the link to the tiger version? > > > > Liat > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer June 2008