Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

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 >

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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 >

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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

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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

Prob:Software Download Tiger version \
by Liat Levita 16 Jun '08

16 Jun '08

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

2 1

Re: [Freesurfer] HBM 2008
by Pedro Paulo de Magalhães Oliveira Junior 16 Jun '08

16 Jun '08

There is a very interesting poster using FreeSurfer (174-M) from Marije Jansen (Univ. Nottingham) - "Cortical Thickness and depression in a population-based sample of adolescents." The statistic method used there is very interesting to possibly be added in QDEC. 2008/6/15 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > he's there somewhere :) > > On Sun, 15 Jun 2008, Pedro Paulo de Magalhães Oliveira Junior wrote: > > Hi, >> I think some of us are in Melbourne these days in the HBM. >> >> If somebody is interested in exchanging experiences in FreeSurfer usage we >> can meet somewhere in this event. >> >> Actually I was looking for Doug :) >> >> Regards, >> >> Pedro Paulo Oliveira Jr >> >

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HBM 2008
by Pedro Paulo de Magalhães Oliveira Junior 15 Jun '08

15 Jun '08

Hi, I think some of us are in Melbourne these days in the HBM. If somebody is interested in exchanging experiences in FreeSurfer usage we can meet somewhere in this event. Actually I was looking for Doug :) Regards, Pedro Paulo Oliveira Jr

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question
by Valentina.Durastanti＠uniroma1.it 14 Jun '08

14 Jun '08

Hi, I'm starting to use Freesurfer to analyze SPGRs images and my question is: Do I have to use the average of two images (invol1 + invol2) or I just can use one SPGRs? Thanks Valentina

2 1

Re: [Freesurfer] wiki problem
by Liat Levita 13 Jun '08

13 Jun '08

Hello, hope this helps. The quote from our security engineer regarding this issue. "That Harvard machine was doing what appeared to be shellcode NOPs, which is indicative of someone/something trying an exploit. Our policy on such things is that if we feel this to be a valid threatand we did at the timewe block the IP." Liat ----- Original Message ----- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Date: Friday, June 13, 2008 8:35 am Subject: Re: [Freesurfer] wiki problem > good to know it wasn't something on our end. Any idea what > constituted > "suspicious traffic"? It might be useful for us to know. > > cheers, > Bruce > > > On Fri, 13 Jun 2008, Liat Levita wrote: > > > Dear all, thank you so much for all your help. Problem solved. > Cornell > was blocking the site for a security reasons, our network guys said > they > noticed suspicious traffic from that i.p address (the mind boggles > ...). > They have now unblocked it : ) > Liat > > > > > > > > ----- Original Message ----- > > From: Joe Paxton <jpaxton(a)wjh.harvard.edu> > > Date: Wednesday, June 11, 2008 9:34 am > > Subject: Re: [Freesurfer] wiki problem > > > >> Perhaps it is a DNS issue? You could try bypassing DNS by replacing > >> > >> the hostname with the ip in the URL: > >> > >> http://132.183.202.158/fswiki > >> or > >> https://132.183.202.158/fswiki > >> > >> If that works, then the problem is likely with DNS at Cornell, in > >> which case you'll need to contact your network helpdesk. > >> > >> On Jun 11, 2008, at 8:31 AM, Liat Levita wrote: > >> > >>> Hi Krish, > >>> > >>> I am afraid we had no joy with either option. > >>> > >>> No one in lab can get access, we have used both Mozilla Firefox, > >> and > >>> Internet Explorer, neither can establish a connection. > >>> > >>> We never had a problem before. I have tried making changes to my > >>> computer firewall, again no joy. > >>> > >>> Liat > >>> > >>> > >>> ----- Original Message ----- > >>> From: Krish Subramaniam <krish(a)nmr.mgh.harvard.edu> > >>> Date: Tuesday, June 10, 2008 8:01 pm > >>> Subject: Re: [Freesurfer] wiki problem > >>> > >>>> Liat, > >>>> > >>>> Could you tell us the browser you are using? Because we have been > >>>> using the fswiki without problems. ( and I can access fswiki from > >>>> my > >>>> home, hence we can rule out the case that fswiki is not available > >>>> external to our center ) > >>>> > >>>> https://surfer.nmr.mgh.harvard.edu/fswiki > >>>> > >>>> and > >>>> > >>>> http://surfer.nmr.mgh.harvard.edu/fswiki > >>>> > >>>> both should work with the first one asking you to accept a > >>>> certificate. ( secure http connection ) > >>>> > >>>> -Krish > >>>> > >>>> On Jun 10, 2008, at 6:52 PM, Liat Levita wrote: > >>>>> I am sure you are aware of this problem, but since last week we > >>>> have > >>>>> been unable to access the FreeSurfer wiki > >>>> (http://surfer.nmr.mgh.harvard.edu/docs/index.html > >>>>> ). Is it down for maintenance? and if so when will it be up > again?>>>>> > >>>>> I have just started using FreeSurfer, hence having major > >>>> problems > >>>>> without the freesurfer wiki to guide me along. > >>>>> > >>>>> Thank you so much for you help. > >>>>> > >>>>> L > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> 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 > >>>> > >>> > >>> > >>> _______________________________________________ > >>> 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 > > > > > > >

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