Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

(no subject)
by Erika Portera 25 Mar '19

25 Mar '19

External Email - Use Caution Dear Freesurfer experts, I have difficulty in introducing parts of white matter inside the superficial pial and white. I used control points and modified the white matter volume but without resolution. Do you have any advice? Thank you

2 1

[WARNING: UNSCANNABLE EXTRACTION FAILED]talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***
by Chhavi Yadav 25 Mar '19

25 Mar '19

External Email - Use Caution Hi, I am a beginner to freesurfer. Never used it before. Currently I am working on some dicoms from ADNI that I want to preprocess. But I am getting this 'talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** ' error. I am attaching the error log and other files for your reference. Please help me out. Regards, Chhavi

2 5

mri_gtmpvc on Tau and FDG PET
by miracle ozzoude 25 Mar '19

25 Mar '19

External Email - Use Caution Hello FreeSurfer, I would like to know if mri_gtmpvc for PetSurfer is appropriate for Tau (AV_1451) and FDG pet imaging. Also, is cerebellum a good reference point for both tracers? Thanks. Paul

2 3

Re. Help with TRACULA configuration file
by Yuwen Hung 25 Mar '19

25 Mar '19

External Email - Use Caution Dear TRACULA expert: I wonder if it is recommended to turn on performing of registeration-based B0-inhomogeneity compensation (set dob0 = 1) and utilise the field map magnitude and phase dicom files? The default is set to not to use these functions, but I wonder whether using them may result in better outcomes? Thank you, Yuwen

1 0

Can I process non-human brain mri data by Fressurfer?
by 陈天鸿 25 Mar '19

25 Mar '19

External Email - Use Caution Dear Professor: In my study ,I want to compare the difference and similarity between the sulci on the brains of rats and mice. I hope to use Freesurfer to acquire and compare some specific morphological parameters, such curvature, convexity, geodesic distance and so on. I also want to use this software for landmark-based registration, from which the landmarks on the brain of rats and mice are choosen by myself. So I wonder if the Freesurfer is suitable for me to solve this task? And what I should do? Best regards!

2 1

Gray matter normalized intensity
by Dorothy Sincasto 25 Mar '19

25 Mar '19

External Email - Use Caution Dear Freesurfers Usually, the mean normalized intensity in aseg.stats is not considered important. However, by mistake, I put it in my analysis and found out that the mean intensity of the thalamus explains a lot the variance of my data. What could be the physiological meaning of higher intensity in the thalamus? Could it be associated with either increased myelinization ( more axons or synapses) or with decreased neural soma? Has anybody reported mean normalized intensity effects in subcortical structures? Thanks Dorothy

4 4

error with tract-all. Segmentation fault (core dumped)
by Camerino, .I.L. (Ileana) 25 Mar '19

25 Mar '19

External Email - Use Caution Dear experts of freesurfer, I am using freesurfer for the first time, so apologies in advance if I am asking something it was already answered previously. I looked at previous posts but I could not find an answer. This is what I did: 1 run recon-all on T1 of a single subject, 2 create configuration file 3 run tract all prep 4 moved dmri.bedpostx in the output folder of recon-all 5 run tract all Everything run well until step 5 (tract all), there something goes wrong after tract all but I do not understand what. The only error messages I can see are: "segmentation fault (core dumped)" in the tract all-e file and "trac-paths exited with ERRORS". I read another post with the same issue but it wasn't answered. any advice would be appreciated! Thank you in advance Ileana

1 0

segmentHA_T1_long.sh error
by Daniel Callow 25 Mar '19

25 Mar '19

External Email - Use Caution Hello, When trying to run the segmentHA_T1_long.sh command on my data I get the following error log posted below (I ran several versions of a for loop and got issues with all of them). I closed out the matlab browsers and am retrying the code again to see if it is reproducible and so afar it is running. I just wanted to get an idea if this is a known problem. Best, Daniel ------------------------------------------------------------------------ Segmentation violation detected at Sat Mar 23 18:31:18 2019 ------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Current Visual : Quartz Default Encoding : ISO-8859-1 MATLAB Architecture: maci64 MATLAB Root : /Applications/freesurfer_dev/MCRv84 MATLAB Version : 8.4.0.150421 (R2014b) Operating System : Darwin 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64 Processor ID : x86 Family 6 Model 44 Stepping 2, GenuineIntel Software OpenGL : 0 Virtual Machine : Java 1.7.0_55-b13 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode Window System : Quartz Fault Count: 1 Abnormal termination: Segmentation violation Register State (from fault): RAX = 00007f9c4806f000 RBX = 00007f9c4806f000 RCX = 0000700009ab52d0 RDX = 000000011392e97e RSP = 00007f9c4806f000 RBP = 00009b6309ab52d0 RSI = 00007f9c47637ba0 RDI = 0000000000000000 R8 = 00007f9c4a0a3270 R9 = 00007f9c4806f000 R10 = 000000011e59176a R11 = 0000000000000000 R12 = 0000700009ab5330 R13 = 000000011377c3c7 R14 = 0000700009ab53a0 R15 = 000000011e591777 RIP = 00000001188c5f40 RFL = 00007f9c4a0a3270 CS = 00009b6300305bc3 FS = 000000011e59176a GS = 00007f9c4806f1e8 Stack Trace (from fault): [ 0] 0x00000001075f6e64 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052 [ 1] 0x00000001075faa2a /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906 [ 2] 0x00000001075fa477 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119 [ 3] 0x000000010c443b7a /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146 [ 4] 0x000000010c443e58 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880 [ 5] 0x000000010c441733 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275 [ 6] 0x00007fffbac1cb3a /usr/lib/system/libsystem_platform.dylib+00011066 _sigtramp+00000026 [ 7] 0x000000011377d6f8 /Applications/freesurfer_dev/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03192568 _ZN23JNI_ArgumentPusherVaArg7iterateEy+00000000 [ 8] 0x000000011376dd67 /Applications/freesurfer_dev/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03128679 jni_GetMethodID+00000126 [ 9] 0x000000010f8ca271 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwjmi.dylib+00160369 _Z12mljGetMethodP7_jclassPKcS2_+00000049 [ 10] 0x000000011ddec366 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhg.dylib+00598886 _ZN2ui14JavaScreenData20getPrimaryScreenRectEv+00000150 [ 11] 0x000000011ddf1ef4 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhg.dylib+00622324 _ZN10ScreenImpl13getScreenSizeEv+00000036 [ 12] 0x000000011ddf02e2 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhg.dylib+00615138 _ZNK2ui24RootScreenAndPointerImpl13getScreenSizeEv+00000018 [ 13] 0x000000011ddf4f58 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhg.dylib+00634712 _ZN2ui4Root17getScreenSizeImplEPN4mcos11COSPropInfoEPNS1_9COSClientEPNS1_12COSInterfaceE+00000040 [ 14] 0x000000011e22bd13 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhg.dylib+05053715 _ZN7hgutils6StubPIIN2ui4RootENS_15PropertyStorageIN8graphics8datatype8PositionENS_6NoModeENS_21NoSerializableStorageEEEE8getValueEPN4mcos12COSInterfaceE+00000099 [ 15] 0x000000010d4e9a6e /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00371310 _ZN4mcos13COSInterfaceI18igetDirectInternalEPNS_12COSInterfaceE+00000110 [ 16] 0x000000010d4dfc80 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00330880 _ZN4mcos13COSInterfaceI10igetDirectEPKNS_9COSClientEPNS_12COSInterfaceE+00000128 [ 17] 0x000000010d54f12b /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00786731 _ZN4mcos28getValueOfKnownClassPropertyEP11mxArray_tagmPKS0_NS_15COSInterfacePtrEPKNS_9COSClientE+00000411 [ 18] 0x000000010d550070 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00790640 _ZN4mcos16getPropertyValueEPKNS_9COSClientEPNS_8COSClassEPK11mxArray_tagPKcmPS5_+00000416 [ 19] 0x000000010d550483 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00791683 _ZNK4mcos5GetMI6invokeEPKNS_9COSClientERiPNS_8COSValueEiPKS5_+00000355 [ 20] 0x000000010d5381f2 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00692722 _ZN24OpaqueMethodCallMetaData11callCMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000466 [ 21] 0x000000010d53af4e /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00704334 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000494 [ 22] 0x000000010d538b3e /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00695102 _Z18mcosCallMethodImplN4mcos9COSNameIDES0_PKNS_9COSClientEiPP11mxArray_tagiPPKS4_bb+00000286 [ 23] 0x000000010d539a82 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00699010 _Z12omCallMethodN4mcos9COSNameIDES0_PKNS_9COSClientEiPP11mxArray_tagiPPKS4_b+00000114 [ 24] 0x000000011f59a6c2 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhgutils.dylib+00440002 _ZN7hgutils17MCOSMethodInvoker6invokeEPKN4mcos9COSClientERiPNS1_8COSValueEiPKS6_+00000866 [ 25] 0x000000011f59a220 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhgutils.dylib+00438816 _ZN7hgutils14callMCOSMethodERKN4mcos9COSNameIDERKNS0_12MemberAccessEPNS0_8COSClassEPKNS0_9COSClientERiPNS0_8COSValueEiPKSD_+00000112 [ 26] 0x000000011f59a1a7 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhgutils.dylib+00438695 _ZN7hgutils14callMCOSMethodERKN4mcos9COSNameIDEPNS0_8COSClassEPKNS0_9COSClientERiPNS0_8COSValueEiPKSA_+00000055 [ 27] 0x000000011f580292 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhgutils.dylib+00332434 _ZThn8_NK7hgutils22HGPropHandlerClassInfo16areChildrenSavedEv+00029170 [ 28] 0x000000010d5381f2 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00692722 _ZN24OpaqueMethodCallMetaData11callCMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000466 [ 29] 0x000000010d53af4e /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00704334 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000494 [ 30] 0x000000010d539d41 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00699713 _Z22omCallMethodWithClientP11mxArray_tagbS0_iPS0_iPPKS_PKN4mcos9COSClientEPS8_PPNS5_13COSMethodInfoE+00000417 [ 31] 0x000000010d5c5930 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+01272112 _Z18omCallOpaqueMethodP11mxArray_tagS0_iPS0_iPPKS_+00000112 [ 32] 0x000000011d63b353 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhgbuiltins.dylib+00193363 hgGetWrapper+00000435 [ 33] 0x000000010d370cc6 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00117958 _ZN11Mfh_builtin11dispatch_mfEiPP11mxArray_tagiS2_+00000086 [ 34] 0x000000010d35912d /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00020781 _ZN13Mfh_MATLAB_fn11dispatch_fhEiPP11mxArray_tagiS2_+00000333 [ 35] 0x000000010c716d62 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650 [ 36] 0x000000010c6b8dd8 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01138136 inPcodeWalker+00022552 [ 37] 0x000000010c6b5917 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01124631 inPcodeWalker+00009047 [ 38] 0x000000010c6b0fb7 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935 [ 39] 0x000000010c6b21c6 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01110470 _Z26inExecuteMFunctionOrScriptP6Mfh_mpb+00000886 [ 40] 0x000000010c7541f1 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01774065 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002337 [ 41] 0x000000010d3b5c28 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00400424 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000600 [ 42] 0x000000010d599e8e /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+01093262 _ZNK4mcos17MScopedMethodInfo6invokeEPKNS_9COSClientERiPNS_8COSValueEiPKS5_+00000606 [ 43] 0x000000010d537597 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00689559 _ZN24OpaqueMethodCallMetaData11callMMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000359 [ 44] 0x000000010d53ae63 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00704099 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000259 [ 45] 0x000000010d539d41 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00699713 _Z22omCallMethodWithClientP11mxArray_tagbS0_iPS0_iPPKS_PKN4mcos9COSClientEPS8_PPNS5_13COSMethodInfoE+00000417 [ 46] 0x000000010d5c5ee8 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+01273576 _Z18omCallStaticMethodP11mxArray_tagiPS0_iPPKS_+00000088 [ 47] 0x000000010d64ee64 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+01834596 _ZN17Mfh_opaque_static11dispatch_mfEiPP11mxArray_tagiS2_+00000116 [ 48] 0x000000010d35912d /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00020781 _ZN13Mfh_MATLAB_fn11dispatch_fhEiPP11mxArray_tagiS2_+00000333 [ 49] 0x000000010d64bacc /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+01821388 _ZN10Mfh_opaque11dispatch_fhEiPP11mxArray_tagiS2_+00000028 [ 50] 0x000000010c716d62 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650 [ 51] 0x000000010c66c59e /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+00824734 inCallFcnFromReference+00000110 [ 52] 0x000000010c6b5003 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01122307 inPcodeWalker+00006723 [ 53] 0x000000010c6b0fb7 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935 [ 54] 0x000000010c6b21c6 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01110470 _Z26inExecuteMFunctionOrScriptP6Mfh_mpb+00000886 [ 55] 0x000000010c7541f1 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01774065 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002337 [ 56] 0x000000010d3b5c55 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00400469 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000645 [ 57] 0x000000010c716d62 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650 [ 58] 0x000000010c6b8dd8 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01138136 inPcodeWalker+00022552 [ 59] 0x000000010c6b5702 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01124098 inPcodeWalker+00008514 [ 60] 0x000000010c6b0fb7 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935 [ 61] 0x000000010c6b0cad /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105069 inInterPcode+00000157 [ 62] 0x000000010c6a7b9f /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01067935 _ZN12InterpBridge33DoMatlabFcnCallInDesiredWorkspaceEiPP11mxArray_tagiPPKS0_P13Mfh_MATLAB_fnP15inWorkSpace_tag+00004015 [ 63] 0x000000010c6a9a79 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01075833 _Z25in_local_call_with_setjmpIN5boost3_bi6bind_tIvPFvPiP12_pcodeheaderS3_PP11mxArray_tag12inDebugCheckENS1_5list5INS1_5valueIS3_EENSD_IS5_EENS0_3argILi1EEENSG_ILi2EEENSD_IS9_EEEEEEEN6mlutil14cmddistributor17inExecutionStatusET_S3_S8_b+00000073 [ 64] 0x000000010c6a528d /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01057421 _Z12inEvalStringP15_memory_contextRKSbItSt11char_traitsItESaItEE8EvalTypeiPP11mxArray_tag12inDebugCheckP12_pcodeheaderPib+00002877 [ 65] 0x000000010c6a57cd /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01058765 _ZN12InterpBridge22EvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEPibb+00000141 [ 66] 0x000000010c6a5c05 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01059845 _ZN12InterpBridge7EvalCmdERKSbItSt11char_traitsItESaItEEb+00000021 [ 67] 0x000000010c603347 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+00394055 inEvalCmd+00000119 [ 68] 0x000000010c41b7fa /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00223226 _Z16mnRunLoginScriptv+00000586 [ 69] 0x000000010c442f63 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00384867 _Z32mnRunPathDependentInitializationv+00000051 [ 70] 0x000000010c42980c /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00280588 _ZN11mcrInstance26init_on_interpreter_threadEP11MfileReaderP13MexFileReader+00000988 [ 71] 0x000000010c437fb8 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00339896 _ZN5boost6detail8function21function_obj_invoker0INS_3_bi6bind_tIbNS_4_mfi3mf2Ib11mcrInstanceP11MfileReaderP13MexFileReaderEENS3_5list3INS3_5valueIPS7_EENSE_IS9_EENSE_ISB_EEEEEEbE6invokeERNS1_15function_bufferE+00000040 [ 72] 0x000000010c436dc1 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00335297 _ZN3mcr7runtime17InterpreterThread4Impl22TypedInvocationRequestIbE29doNotRethrowMxArrayExceptionsERKN5boost8functionIFbvEEE+00000033 [ 73] 0x000000010c437bd9 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00338905 _ZN5boost6detail11task_objectIbNS_3_bi6bind_tIbPFbRKNS_8functionIFbvEEEENS2_5list1INS2_5valueIS6_EEEEEEE6do_runEv+00000025 [ 74] 0x000000010c437276 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00336502 _ZN5boost6detail9task_baseIbE3runEv+00000166 [ 75] 0x000000010c437067 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00335975 _ZN3mcr7runtime17InterpreterThread4Impl22TypedInvocationRequestIbE3runEv+00000023 [ 76] 0x000000010c401f90 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00118672 _ZN3mcr7runtime17InterpreterThread4Impl26invocation_request_handlerEl+00000032 [ 77] 0x0000000105114005 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwservices.dylib+00196613 _ZN10eventqueue18UserEventQueueImpl5flushEv+00001205 [ 78] 0x000000010dbeba65 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwuix.dylib+00043621 _Z25isHandleUserEventCallbackPFvPvE+00000501 [ 79] 0x00000001051e3a45 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwservices.dylib+01047109 _Z21svWS_ProcessCallbacksv+00016693 [ 80] 0x00000001051df152 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwservices.dylib+01028434 _Z25svWS_ProcessPendingEventsiib+00000834 [ 81] 0x00000001051dee5e /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwservices.dylib+01027678 _Z25svWS_ProcessPendingEventsiib+00000078 [ 82] 0x000000010c40218f /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095 [ 83] 0x000000010c40249f /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335 [ 84] 0x000000010c3e8d1b /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059 [ 85] 0x00007fffbac2693b /usr/lib/system/libsystem_pthread.dylib+00014651 _pthread_body+00000180 [ 86] 0x00007fffbac26887 /usr/lib/system/libsystem_pthread.dylib+00014471 _pthread_body+00000000 [ 87] 0x00007fffbac2608d /usr/lib/system/libsystem_pthread.dylib+00012429 thread_start+00000013 If this problem is reproducible, please submit a Service Request via: http://www.mathworks.com/support/contact_us/ A technical support engineer might contact you with further information. Thank you for your help. *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***
by Chhavi Yadav 25 Mar '19

25 Mar '19

External Email - Use Caution Hi, I am a beginner to freesurfer. Currently I am working on some dicoms from ADNI that I want to preprocess using autorecon1. But I am getting this 'talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** ' error. Also I am using v6.0.0. If I use the -notal-check flag, at/after the skull stripping stage I get continuous messages of this sort for different coordinates: left/right detection failed, moving y coord to -2147483638 from -2147483648 I am attaching the error log for your reference without the -notal-check flag. Please help me out. Regards, Chhavi

1 0

mris_fix_topology stuck running
by Soichi Hayashi 24 Mar '19

24 Mar '19

External Email - Use Caution Hello. I am trying to troubleshoot an issue where recon_all is not finishing after >24 hours. It's getting stuck when it tries to run the following command. $ mris_fix_topology -rusage ./output/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 output rh INFO: assuming .mgz format reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading input surface /home/hayashis/Downloads/output/surf/rh.qsphere.nofix... before topology correction, eno=-696 (nv=191488, nf=384368, ne=576552, g=349) reading brain volume from brain... reading wm segmentation from wm... using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 133741 ambiguous faces found in tessellation segmenting defects... 63 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 16 into 0 -merging segment 23 into 0 -merging segment 48 into 0 -merging segment 32 into 22 -merging segment 49 into 47 -merging segment 54 into 51 57 defects to be corrected 0 vertices coincident Computing Initial Surface Statistics -face loglikelihood: -9.3123 (-4.6561) -vertex loglikelihood: -6.5427 (-3.2713) -normal dot loglikelihood: -3.5794 (-3.5794) -quad curv loglikelihood: -6.0564 (-3.0282) Total Loglikelihood : -25.4907 CORRECTING DEFECT 0 (vertices=65141, convex hull=8287, v0=517) --------------- After displaying the last line, the process seems to be stuck running with 100% cpu (single core) for >24 hours until our batch scheduler kills it. I think the issue is with my input data, but it looks clean and well ACPC aligned, and I don't know what's wrong with it. The input image dimensions are 182 x 218 x 182. Does anyone have any suggestion on how to troubleshoot this problem? Thank you, Soichi Hayashi Indiana University

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