Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

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

2 2

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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segmentHA_T1_long.sh: Command not found.
by Daniel Callow 23 Mar '19

23 Mar '19

External Email - Use Caution Hello, I am trying to use the segmentHA_T1_long.sh command on my longitudinal data. I have already run all the previous steps and have even successfully run longHippoSubfieldsT1.sh. However I want to use the segmentHA version to get my hippocampal segmentations. I assume the issue has something to do with the script not being in the FS6.0 version I downloaded? When looking at the literature for installation all I could find was info on installing runtime which I already have. Any help debugging the issue would be greatly appreciated. Below is the code I ran. #!/bin/tcsh setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh foreach subj (MCIP0031 MCIP0032 MCIP0033 MCIP0035 MCIP0036 MCIP0041 MCIP0048 MCIP0052 MCIP0053 MCIP0054 MCIP0055 MCIP0058 MCIP0061) setenv SUBJECTS_DIR /Volumes/DANIEL/freesurfer_MCIP segmentHA_T1_long.sh base_${subj} end I get the following error. [hlhp-105:/Volumes/DANIEL/freesurfer_MCIP] administrator% ./recon-all_longitudinal_hippo.sh segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. *Best,* *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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DK atlas using method
by 杨国元 23 Mar '19

23 Mar '19

External Email - Use Caution Hello FreeSurfer Developers,I'm attempting to using DK atlas as label to mask my global brain index. I found the lh/rh.DKTatlas40.gcs in /freesurfer/average folder. But I don't know how to read this gcs files. Can I convert this file from gcs to gifit or annot version. Then using MRIread or nilabel to read it label files? Guoyuan Yang Center for MRI Research School of Physics Peking University Beijing, China Tel：18800172884 Email：yangguoyuan(a)pku.edu.cn

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help
by Van Ombergen Angelique 22 Mar '19

22 Mar '19

External Email - Use Caution Please unsubscribe me from the mailing list. Best wishes, Angelique > On 22 Mar 2019, at 15:16, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Build stamp missing in current dev release (Hoopes, Andrew) > 2. VT images from pmod to freesurfer (Donatienne Van Weehaeghe) > 3. Re: recon-all error (Daniel Callow) > 4. Gray matter normalized intensity (Dorothy Sincasto) > 5. Re: Gray matter normalized intensity (Glasser, Matthew) > 6. Re: Gray matter normalized intensity (Bruce Fischl) > 7. help ( Lance ) > 8. recon-all could not read surface file error (Daniel Callow) > 9. Re: help (Bruce Fischl) > 10. Re: recon-all could not read surface file error (Bruce Fischl) > 11. Cerebellum within the pial surface (Matthieu VANHOUTTE) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 21 Mar 2019 16:43:13 +0000 > From: "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Build stamp missing in current dev release > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <5698A83B-BBA5-4EB7-A96F-CC515378666C(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Baxter, this is a bug. Thanks for pointing it out, I'll fix it now. > Andrew > > ?On 3/20/19, 2:43 PM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Baxter P. Rogers" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of baxter.rogers(a)vanderbilt.edu> wrote: > > External Email - Use Caution > > This one: > https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-linux… > The build-stamp.txt file currently contains "freesurfer" with no version > info. It used to be something like > "freesurfer-linux-centos7_x86_64-dev-20181114-4f05c76" which is > considerably more helpful :) > > Thanks much, > Baxter > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > ------------------------------ > > Message: 2 > Date: Thu, 21 Mar 2019 12:49:54 -0400 > From: Donatienne Van Weehaeghe <donatiennevanweehaeghe(a)gmail.com> > Subject: [Freesurfer] VT images from pmod to freesurfer > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CA+W1dKxXS5FjNhYxerphn6RJcc5Jf0Sf_KjoBT6o74iEk4akQw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Dear, > > > I encountered a problem when going from pmod to freesurfer. > > > I made Vt images in pmod using the logan plot, then I used the following > commands to convert them to freesurfer space: > > > > #flirt -noresample -in > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii > -ref > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/T1-2mm_skullstripped.nii.gz > -applyxfm -init > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUV.lrrev_lin_T1.mat > -out > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii > > #3dresample -master > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/occipital.nii.gz > -inset > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii > -prefix > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii > > > > Then I did partial volume correction using this command: > > #mri_gtmpvc --i > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii > --reg Vt.reg.lta --psf 5 --seg > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz > --default-seg-merge --auto-mask 5 0.01 --rbv --o > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg > --no-rescale --threads 8 > > > > > > Then I did surface projection: > > #mri_vol2surf --mov > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz > --reg > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta > --hemi lh --projfrac 0.5 --o > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/lh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz > --cortex --trgsubject fsaverage > > #mri_vol2surf --mov > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz > --reg > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta > --hemi rh --projfrac 0.5 --o > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz > --cortex --trgsubject fsaverage > > > > followed by smoothing, concatening and then a group comparison. However > then I obtained the following error: > > ERROR: cannot find > /usr/local/freesurfer/stable6_0_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/pos/th13/mc-z.csd > > > Kind regards > > Donatienne >

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Cerebellum within the pial surface
by Matthieu VANHOUTTE 22 Mar '19

22 Mar '19

External Email - Use Caution Dear FreeSurfer's experts, I encountered one problem following a recon-all: small part of the gray matter cerebellum has been taken as cortical gray matter within the occipital pial surface (see image attached below on right hemisphere). How could I correct for this defect? Best, Matthieu

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