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30132 discussions

Freesurfer cortical parcellation not covering gray matter in depth
by Yixin Ma 31 Oct '18

31 Oct '18

External Email - Use Caution Hi Bruce, Thanks for your reply to ask me to check lh.pial and rh.pial. I checked and they look good to me as attached picture. Another information is that cortical layers that I generated from the freesurfer recon-all look good as well. So it seems like the problem is only on cortical parcellation? Do you have any other suggestions on what I can check or is there any parameters that I can tune to make cortical parcellation better? Best regards, Yixin [image: Screen Shot 2018-10-27 at 5.28.33 PM.png] [image: Screen Shot 2018-10-30 at 11.44.05 AM.png]

2 1

preproc-sess not passing custom instem to rawfunc2surf-sess
by Jacob Matthews 31 Oct '18

31 Oct '18

External Email - Use Caution Hi FS Team, We've tried running preproc-sess using a custom instem, but it fails at rawfunc2surf-sess. From parsing the code a bit, it appears that while most of the x-sess scripts called in preproc-sess pass their respective outstem's as the instem to the subsequent function, rawfunc2sess is never given an explicit instem and instead builds up its instem based on assumptions from the provided flags. So while our stc-sess outstem according to the log was "fmcpricor.odd" (based on a custom instem "fmcpricor", followed by no mc-sess, and stc-sess), our rawfunc2surf-sess instem defaulted to "fmcpr.odd". Similarly it will also miss some other flags given to preproc-sess. For example, the -nomc flag passed to preproc-sess will not effect rawfunc2surf-sess instem, as it adds "mcpr" to the proposed instem based on the -per-run flag, and does not take the -nomc flag into account. So any preproc-sess calls using -nomc will fail at rawfunc2surf-sess. Am I interpreting this correctly? My assumption is that I will either need to add instem passing to my local preproc-sess file, or otherwise call each of the x-sess scripts directly in my own script rather than using preproc-sess? Thanks, Jacob Matthews MRI Specialist Rotman Research Institute Baycrest Hospital 416-785-2500 ext. 3322

1 0

Options to decrease computation time
by Gregory Book 31 Oct '18

31 Oct '18

External Email - Use Caution I'm curious if there are options to decrease computation time, even at the expense of quality?

3 2

Fwd: Improved segmentation using 3D FLAIR
by Lee Ho Jun 31 Oct '18

31 Oct '18

External Email - Use Caution Hello freesurfer users. I am a radiologist, who is trying to setup a protocol for freesurfer segmentation. I came to know that with 3D T2 weighted images, or 3D FLAIR images, I can get better surface segmentations, and based on search of previous archives of the mailing list, I found that 3D FLAIR images may give better segmentations. My question is that whether applying fat suppression will change the results, since, fat suppression tends to lead to signal dropouts in areas of high susceptibility changes, such as near mastoid air cells. Also, I am a little confused about the bandwidth matched protocols, will "matching" the bandwidths suffice? Best wishes, Ho-Joon Lee.

2 1

Postdoctoral Position at the University of Zurich in Switzerland
by Nicolas Langer 31 Oct '18

31 Oct '18

External Email - Use Caution Description of the lab: The Methods of Plasticity Lab in the Department of Psychology (http://www.psychology.uzh.ch/en/chairs/plafor.html) is focussed on creating novel methods to advance the understanding about neuronal plasticity, and the mechanisms for stabilization and compensation across the lifespan. For this we utilize data of various sources, including (but not restricted to) EEG, fMRI, MRI, eye-tracking, every-day behavioral data, video, and motion sensing to apply state of the art machine learning methods to these data. Topic-wise, we focus on the assessment of cognitive functioning, including perceptual processing, learning, (working-) memory, decision-making and processing speed. We highly value interdisciplinary discourse, scientific integrity and strongly support the Open Science movement. Responsibilities: The successful candidate will work on research in large scale multimodal projects in the field of healthy aging and developmental disorders. The candidate will take part in ongoing projects or initiate new research within the team of Prof. Nicolas Langer, closely collaborating with the URPP Dynamics of Healthy Aging (UZH), the HBN of the Child Mind Institute, New York and the Systems Group (ETHZ). Main responsibilities include the development of open-source analysis tools, analysis of data, dissemination of study results in peer reviewed journals, and the supervision of PhD, MA and BA students. Workload %: 80 - 100% Qualifications: PhD degree in a field related to cognitive neuroscience (e.g., cognitive neuroscience, neuroscience, (neuro-)psychology, developmental psychology, medicine, electrical engineering, biomedical engineering or computer science) Proficiency in programming in Matlab (or R, Python) Solid knowledge about statistical methods including machine learning Strong research background in the design of neurophysiological experiments Excellent verbal and written English skills Previous experience in developing analysis methods for EEG, fMRI, MRI data is desirable Experience with EEG analyses programs (e.g., EEGLAB, brainstorm) are desirable Interest in teaching about methods (e.g. analysis of EEG data) are a plus Language requirements: English We offer: To work in a team of highly motivated young researchers who are passionate about neuroscience, psychology and computer science A very competitive salary and generous social benefits Generous support for professional travel and research needs An inspiring work environment within the Department of Psychology and the University of Zurich The opportunity to live in Zurich one of the world’s most attractive cities Please visit https://www.pa.uzh.ch/en/Willkommen-an-der-UZH.html for further information. This position opens on: February 1st, 2019 More information: Prof. Nicolas Langer, n.langer(a)psychologie.uzh.ch Application To be considered please stick to the following application format: - CV including publication list and contact details of two referees (max. 3 pages) - Statement describing motivations, personal qualifications and research interests (max. 2 pages) - Save application in one single pdf file with the file name “Methlab_[SURNAME]_[name].pdf” - Send application by email to n.langer(a)psychologie.uzh Applications will be considered until the position is filled. Nicolas Langer Assistant Professor of Methods of Plasticity Research University of Zurich Andreasstrasse 15 (Office AND.4.58) 8050, Zurich, Switzerland n.langer(a)psychologie.uzh.ch phone: (+41) 44 635 34 14 http://www.psychology.uzh.ch/en/areas/nec/plafor.html

1 0

error in hippocampal subfields and nuclei of amygdala segmentation
by 오진영 31 Oct '18

31 Oct '18

External Email - Use Caution Dear freesurfer experts, I'm trying to run segmentation of hippocampal subfields and nuclei of amygdala with segmentHA_T1.sh command. I already run segmentation of hippocampal subfields and nuclei of amygdala several times, however, after segment nuclei of amygdala in left hemisphere and before segment nuclei of amygdala in right hemisphere, there appears same error "MATLAB is exiting because of fatal error" and hippocampal subfields segmentation stops. Ignoring and Trying the same command few more times, I can make it to segment subfields of amygdala, but I am still wondering if I can run segmentHA_T1.sh without any error. Following is the repeated error with the few lines: #-------------------------------------------- #@# Hippocampal Subfields processing (T1) right 2018년 10월 30일 화요일 14시 07분 17초 KST ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer/MCRv84//sys/os/maci64:/Applications/freesurfer/lib/gcc/lib: PostVMInit failed to initialize com.mathworks.mwswing.MJStartupForDesktop ------------------------------------------------------------------------ Segmentation violation detected at Tue Oct 30 14:07:20 2018 ------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Current Visual : Quartz Default Encoding : US-ASCII MATLAB Architecture: maci64 MATLAB Root : /Applications/freesurfer/MCRv84 MATLAB Version : 8.4.0.150421 (R2014b) Operating System : Darwin 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64 Processor ID : x86 Family 6 Model 158 Stepping 9, 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: 2 Abnormal termination: Segmentation violation Register State (from fault): RAX = 00007fafcba4f000 RBX = 00007fafcba4f000 RCX = 000070000cdf72d0 RDX = 0000000111cba97e RSP = 00007fafcba4f000 RBP = 00009b630cdf72d0 RSI = 00007fafcdb8a9b0 RDI = 0000000000000000 R8 = 00007fafcc2dc270 R9 = 00007fafcba4f000 R10 = 000000011bd1f76a R11 = 0000000000000000 R12 = 000070000cdf7330 R13 = 0000000111b083c7 R14 = 000070000cdf73a0 R15 = 000000011bd1f777 RIP = 0000000116ca6f40 RFL = 00007fafcc2dc270 CS = 00009b6300305bc3 FS = 000000011bd1f76a GS = 00007fafcba4f1e8 Stack Trace (from fault): [ 0] 0x0000000105f76e64 /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052 [ 1] 0x0000000105f7aa2a /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906 [ 2] 0x0000000105f7a477 /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119 [ 3] 0x000000010d041b7a /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146 [ 4] 0x000000010d041e58 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880 [ 5] 0x000000010d03f733 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275 [ 6] 0x00007fff74b75f5a /usr/lib/system/libsystem_platform.dylib+00008026 _sigtramp+00000026 [ 7] 0x0000000111b096f8 /Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03192568 _ZN23JNI_ArgumentPusherVaArg7iterateEy+00000000 [ 8] 0x0000000111af9d67 /Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03128679 jni_GetMethodID+00000126 [ 9] 0x00000001104dd271 /Applications/freesurfer/MCRv84//bin/maci64/libmwjmi.dylib+00160369 _Z12mljGetMethodP7_jclassPKcS2_+00000049 [ 10] 0x000000011b57a366 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00598886 _ZN2ui14JavaScreenData20getPrimaryScreenRectEv+00000150 [ 11] 0x000000011b57fef4 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00622324 _ZN10ScreenImpl13getScreenSizeEv+00000036 [ 12] 0x000000011b57e2e2 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00615138 _ZNK2ui24RootScreenAndPointerImpl13getScreenSizeEv+00000018 [ 13] 0x000000011b582f58 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00634712 _ZN2ui4Root17getScreenSizeImplEPN4mcos11COSPropInfoEPNS1_9COSClientEPNS1_12COSInterfaceE+00000040 [ 14] 0x000000011b9b9d13 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+05053715 _ZN7hgutils6StubPIIN2ui4RootENS_15PropertyStorageIN8graphics8datatype8PositionENS_6NoModeENS_21NoSerializableStorageEEEE8getValueEPN4mcos12COSInterfaceE+00000099 [ 15] 0x000000010e0e7a6e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00371310 _ZN4mcos13COSInterfaceI18igetDirectInternalEPNS_12COSInterfaceE+00000110 [ 16] 0x000000010e0ddc80 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00330880 _ZN4mcos13COSInterfaceI10igetDirectEPKNS_9COSClientEPNS_12COSInterfaceE+00000128 [ 17] 0x000000010e14d12b /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00786731 _ZN4mcos28getValueOfKnownClassPropertyEP11mxArray_tagmPKS0_NS_15COSInterfacePtrEPKNS_9COSClientE+00000411 [ 18] 0x000000010e14e070 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00790640 _ZN4mcos16getPropertyValueEPKNS_9COSClientEPNS_8COSClassEPK11mxArray_tagPKcmPS5_+00000416 [ 19] 0x000000010e14e483 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00791683 _ZNK4mcos5GetMI6invokeEPKNS_9COSClientERiPNS_8COSValueEiPKS5_+00000355 [ 20] 0x000000010e1361f2 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00692722 _ZN24OpaqueMethodCallMetaData11callCMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000466 [ 21] 0x000000010e138f4e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00704334 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000494 [ 22] 0x000000010e136b3e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00695102 _Z18mcosCallMethodImplN4mcos9COSNameIDES0_PKNS_9COSClientEiPP11mxArray_tagiPPKS4_bb+00000286 [ 23] 0x000000010e137a82 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00699010 _Z12omCallMethodN4mcos9COSNameIDES0_PKNS_9COSClientEiPP11mxArray_tagiPPKS4_b+00000114 [ 24] 0x000000011cd286c2 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00440002 _ZN7hgutils17MCOSMethodInvoker6invokeEPKN4mcos9COSClientERiPNS1_8COSValueEiPKS6_+00000866 [ 25] 0x000000011cd28220 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00438816 _ZN7hgutils14callMCOSMethodERKN4mcos9COSNameIDERKNS0_12MemberAccessEPNS0_8COSClassEPKNS0_9COSClientERiPNS0_8COSValueEiPKSD_+00000112 [ 26] 0x000000011cd281a7 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00438695 _ZN7hgutils14callMCOSMethodERKN4mcos9COSNameIDEPNS0_8COSClassEPKNS0_9COSClientERiPNS0_8COSValueEiPKSA_+00000055 [ 27] 0x000000011cd0e292 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00332434 _ZThn8_NK7hgutils22HGPropHandlerClassInfo16areChildrenSavedEv+00029170 [ 28] 0x000000010e1361f2 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00692722 _ZN24OpaqueMethodCallMetaData11callCMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000466 [ 29] 0x000000010e138f4e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00704334 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000494 [ 30] 0x000000010e137d41 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00699713 _Z22omCallMethodWithClientP11mxArray_tagbS0_iPS0_iPPKS_PKN4mcos9COSClientEPS8_PPNS5_13COSMethodInfoE+00000417 [ 31] 0x000000010e1c3930 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01272112 _Z18omCallOpaqueMethodP11mxArray_tagS0_iPS0_iPPKS_+00000112 [ 32] 0x000000011adc9353 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgbuiltins.dylib+00193363 hgGetWrapper+00000435 [ 33] 0x000000010df6ecc6 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00117958 _ZN11Mfh_builtin11dispatch_mfEiPP11mxArray_tagiS2_+00000086 [ 34] 0x000000010df5712d /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00020781 _ZN13Mfh_MATLAB_fn11dispatch_fhEiPP11mxArray_tagiS2_+00000333 [ 35] 0x000000010d314d62 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650 [ 36] 0x000000010d2b6dd8 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01138136 inPcodeWalker+00022552 [ 37] 0x000000010d2b3917 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01124631 inPcodeWalker+00009047 [ 38] 0x000000010d2aefb7 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935 [ 39] 0x000000010d2b01c6 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01110470 _Z26inExecuteMFunctionOrScriptP6Mfh_mpb+00000886 [ 40] 0x000000010d3521f1 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01774065 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002337 [ 41] 0x000000010dfb3c28 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00400424 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000600 [ 42] 0x000000010e197e8e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01093262 _ZNK4mcos17MScopedMethodInfo6invokeEPKNS_9COSClientERiPNS_8COSValueEiPKS5_+00000606 [ 43] 0x000000010e135597 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00689559 _ZN24OpaqueMethodCallMetaData11callMMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000359 [ 44] 0x000000010e138e63 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00704099 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000259 [ 45] 0x000000010e137d41 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00699713 _Z22omCallMethodWithClientP11mxArray_tagbS0_iPS0_iPPKS_PKN4mcos9COSClientEPS8_PPNS5_13COSMethodInfoE+00000417 [ 46] 0x000000010e1c3ee8 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01273576 _Z18omCallStaticMethodP11mxArray_tagiPS0_iPPKS_+00000088 [ 47] 0x000000010e24ce64 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01834596 _ZN17Mfh_opaque_static11dispatch_mfEiPP11mxArray_tagiS2_+00000116 [ 48] 0x000000010df5712d /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00020781 _ZN13Mfh_MATLAB_fn11dispatch_fhEiPP11mxArray_tagiS2_+00000333 [ 49] 0x000000010e249acc /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01821388 _ZN10Mfh_opaque11dispatch_fhEiPP11mxArray_tagiS2_+00000028 [ 50] 0x000000010d314d62 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650 [ 51] 0x000000010d26a59e /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+00824734 inCallFcnFromReference+00000110 [ 52] 0x000000010d2b3003 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01122307 inPcodeWalker+00006723 [ 53] 0x000000010d2aefb7 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935 [ 54] 0x000000010d2b01c6 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01110470 _Z26inExecuteMFunctionOrScriptP6Mfh_mpb+00000886 [ 55] 0x000000010d3521f1 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01774065 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002337 [ 56] 0x000000010dfb3c55 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00400469 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000645 [ 57] 0x000000010d314d62 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650 [ 58] 0x000000010d2b6dd8 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01138136 inPcodeWalker+00022552 [ 59] 0x000000010d2b3702 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01124098 inPcodeWalker+00008514 [ 60] 0x000000010d2aefb7 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935 [ 61] 0x000000010d2aecad /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105069 inInterPcode+00000157 [ 62] 0x000000010d2a5b9f /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01067935 _ZN12InterpBridge33DoMatlabFcnCallInDesiredWorkspaceEiPP11mxArray_tagiPPKS0_P13Mfh_MATLAB_fnP15inWorkSpace_tag+00004015 [ 63] 0x000000010d2a7a79 /Applications/freesurfer/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] 0x000000010d2a328d /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01057421 _Z12inEvalStringP15_memory_contextRKSbItSt11char_traitsItESaItEE8EvalTypeiPP11mxArray_tag12inDebugCheckP12_pcodeheaderPib+00002877 [ 65] 0x000000010d2a37cd /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01058765 _ZN12InterpBridge22EvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEPibb+00000141 [ 66] 0x000000010d2a3c05 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01059845 _ZN12InterpBridge7EvalCmdERKSbItSt11char_traitsItESaItEEb+00000021 [ 67] 0x000000010d201347 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+00394055 inEvalCmd+00000119 [ 68] 0x000000010d0197fa /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00223226 _Z16mnRunLoginScriptv+00000586 [ 69] 0x000000010d040f63 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00384867 _Z32mnRunPathDependentInitializationv+00000051 [ 70] 0x000000010d02780c /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00280588 _ZN11mcrInstance26init_on_interpreter_threadEP11MfileReaderP13MexFileReader+00000988 [ 71] 0x000000010d035fb8 /Applications/freesurfer/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] 0x000000010d034dc1 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00335297 _ZN3mcr7runtime17InterpreterThread4Impl22TypedInvocationRequestIbE29doNotRethrowMxArrayExceptionsERKN5boost8functionIFbvEEE+00000033 [ 73] 0x000000010d035bd9 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00338905 _ZN5boost6detail11task_objectIbNS_3_bi6bind_tIbPFbRKNS_8functionIFbvEEEENS2_5list1INS2_5valueIS6_EEEEEEE6do_runEv+00000025 [ 74] 0x000000010d035276 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00336502 _ZN5boost6detail9task_baseIbE3runEv+00000166 [ 75] 0x000000010d035067 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00335975 _ZN3mcr7runtime17InterpreterThread4Impl22TypedInvocationRequestIbE3runEv+00000023 [ 76] 0x000000010cffff90 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00118672 _ZN3mcr7runtime17InterpreterThread4Impl26invocation_request_handlerEl+00000032 [ 77] 0x00000001053fd005 /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+00196613 _ZN10eventqueue18UserEventQueueImpl5flushEv+00001205 [ 78] 0x000000010e7e9a65 /Applications/freesurfer/MCRv84//bin/maci64/libmwuix.dylib+00043621 _Z25isHandleUserEventCallbackPFvPvE+00000501 [ 79] 0x00000001054cca45 /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01047109 _Z21svWS_ProcessCallbacksv+00016693 [ 80] 0x00000001054c8152 /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01028434 _Z25svWS_ProcessPendingEventsiib+00000834 [ 81] 0x00000001054c7e5e /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01027678 _Z25svWS_ProcessPendingEventsiib+00000078 [ 82] 0x000000010d00018f /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095 [ 83] 0x000000010d00049f /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335 [ 84] 0x000000010cfe6d1b /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059 [ 85] 0x00007fff74b7f661 /usr/lib/system/libsystem_pthread.dylib+00013921 _pthread_body+00000340 [ 86] 0x00007fff74b7f50d /usr/lib/system/libsystem_pthread.dylib+00013581 _pthread_body+00000000 [ 87] 0x00007fff74b7ebf9 /usr/lib/system/libsystem_pthread.dylib+00011257 thread_start+00000013 Abnormal termination: Segmentation violation Register State (from fault): RAX = 00007fafcba4f000 RBX = 00007fafcba4f000 RCX = 000070000cdff9e0 RDX = 0000000111cba97e RSP = 00007fafcba4f000 RBP = 00009b630cdff9e0 RSI = 00007fafcdb8a9b0 RDI = 0000000000000000 R8 = 00007fafcc2dc270 R9 = 00007fafcba4f000 R10 = 000000011bd1f76a R11 = 0000000000000000 R12 = 000070000cdffa40 R13 = 0000000111b083c7 R14 = 000070000cdffab0 R15 = 000000011bd1f777 RIP = 0000000116ca6f40 RFL = 00007fafcc2dc270 CS = 00009b6300305bc3 FS = 000000011bd1f76a GS = 00007fafcba4f1e8 Stack Trace (from fault): [ 0] 0x0000000105f76e64 /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052 [ 1] 0x0000000105f7aa2a /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906 [ 2] 0x0000000105f7a477 /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119 [ 3] 0x000000010d041b7a /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146 [ 4] 0x000000010d041e58 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880 [ 5] 0x000000010d03f733 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275 [ 6] 0x00007fff74b75f5a /usr/lib/system/libsystem_platform.dylib+00008026 _sigtramp+00000026 [ 7] 0x0000000111b096f8 /Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03192568 _ZN23JNI_ArgumentPusherVaArg7iterateEy+00000000 [ 8] 0x0000000111af9d67 /Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03128679 jni_GetMethodID+00000126 [ 9] 0x00000001104dd271 /Applications/freesurfer/MCRv84//bin/maci64/libmwjmi.dylib+00160369 _Z12mljGetMethodP7_jclassPKcS2_+00000049 [ 10] 0x000000011b57a366 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00598886 _ZN2ui14JavaScreenData20getPrimaryScreenRectEv+00000150 [ 11] 0x000000011b57f23a /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00619066 _ZN10gbtobjects10ScreenData14getScreenWidthEv+00000010 [ 12] 0x000000011b5961a6 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00713126 _ZN2ui9container9Container16getChildRefFrameEv+00000038 [ 13] 0x000000011b59655e /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00714078 _ZN2ui9container9Container20fillInUpdateViewInfoERN7hgutils14UpdateViewInfoE+00000046 [ 14] 0x000000011b5834d6 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00636118 _ZN2ui4Root20fillInUpdateViewInfoERN7hgutils14UpdateViewInfoE+00000022 [ 15] 0x000000011b57e79a /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00616346 _ZN10gbtobjects13UpdateVisitor5applyERN2ui4RootE+00000218 [ 16] 0x000000011b693f9a /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+01752986 _ZN10gbtobjects20CommitUpdatesManager13performUpdateEv+00000122 [ 17] 0x000000011b69407b /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+01753211 _ZN10gbtobjects20CommitUpdatesManager24commitAllDatabaseUpdatesEbb+00000027 [ 18] 0x00000001054df7c8 /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01124296 _Z26svWS_CommitDatabaseUpdates27svCommitDatabaseUpdatesType+00000152 [ 19] 0x00000001054c7e2f /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01027631 _Z25svWS_ProcessPendingEventsiib+00000031 [ 20] 0x000000010d00018f /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095 [ 21] 0x000000010d00049f /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335 [ 22] 0x000000010cfe6d1b /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059 [ 23] 0x00007fff74b7f661 /usr/lib/system/libsystem_pthread.dylib+00013921 _pthread_body+00000340 [ 24] 0x00007fff74b7f50d /usr/lib/system/libsystem_pthread.dylib+00013581 _pthread_body+00000000 [ 25] 0x00007fff74b7ebf9 /usr/lib/system/libsystem_pthread.dylib+00011257 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.** This crash report has been saved to disk as /Users/mnd_mac/matlab_crash_dump.49812-2 ** MATLAB is exiting because of fatal error /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 37: 49812 Killed: 9 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args Darwin MnD-macui-iMac.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64 Do I need to request to mathworks? If you have any recommendation, please send me mail back. Thanks a lot! and I hope you to have a good day! Jinyoung

2 4

Segmentation of thalamic nuclei - no reticular nucleus
by Hyun Seok Kim 30 Oct '18

30 Oct '18

External Email - Use Caution Dear all, I ran thalamic nuclei segmentation tool using the "freesurfer-darwin-OSX-ElCapitan-dev-20180919-4c582fa" version. The segmented thalamic nuclei were visualized well by FreeView and were able to find most nuclei. But there is no reticular nucleus (R). I also checked the existence of the reticular nucleus with the following matlab code, but it did not exist. y = MRIread('ThalamicNuclei.v10.T1.FSvoxelSpace.mgz'); find(y.vol == 8125) Is there any way to find the reticular nucleus? Best regards, Hyun Seok Kim

2 1

Third party dependencies directory not found when building from source
by Christian Lee Mcdaniel 30 Oct '18

30 Oct '18

External Email - Use Caution Hello Developers, I am attempting to build Freesurfer from source on my Ubuntu 18.04.1 LTS machine. I have followed the instructions on the freesurfer_linux_developers<http://freesurfer.net/fswiki/freesurfer_linux_developers_page> wiki, and have successfully gotten through steps 1 and 2. However, when trying to install the third party dependencies at step 3 via wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x…, I get the following response: ~$ wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x… --2018-10-30 21:25:16-- ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x… => ‘centos6-x86_64-packages.tar.gz’ Resolving surfer.nmr.mgh.harvard.edu<http://surfer.nmr.mgh.harvard.edu/> (surfer.nmr.mgh.harvard.edu<http://surfer.nmr.mgh.harvard.edu/>)... 132.183.240.105 FreeSurfer<http://surfer.nmr.mgh.harvard.edu/> surfer.nmr.mgh.harvard.edu FreeSurfer Software Suite An open source software suite for processing and analyzing (human) brain MRI images. Skullstripping; Image Registration FreeSurfer<http://surfer.nmr.mgh.harvard.edu/> surfer.nmr.mgh.harvard.edu FreeSurfer Software Suite An open source software suite for processing and analyzing (human) brain MRI images. Skullstripping; Image Registration Connecting to surfer.nmr.mgh.harvard.edu<http://surfer.nmr.mgh.harvard.edu/> (surfer.nmr.mgh.harvard.edu<http://surfer.nmr.mgh.harvard.edu/>)|132.183.240.105|:21... connected. FreeSurfer<http://surfer.nmr.mgh.harvard.edu/> surfer.nmr.mgh.harvard.edu FreeSurfer Software Suite An open source software suite for processing and analyzing (human) brain MRI images. Skullstripping; Image Registration FreeSurfer<http://surfer.nmr.mgh.harvard.edu/> surfer.nmr.mgh.harvard.edu FreeSurfer Software Suite An open source software suite for processing and analyzing (human) brain MRI images. Skullstripping; Image Registration Logging in as anonymous ... Logged in! ==> SYST ... done. ==> PWD ... done. ==> TYPE I ... done. ==> CWD (1) /pub/dist/fs_supportlibs/prebuilt/centos6_x86_64 ... No such directory ‘pub/dist/fs_supportlibs/prebuilt/centos6_x86_64’. I looked in the pub/dist directory and there is no folder named ‘fsl_supportlibs’. I found a file ‘freesurfer-linux-centos6_x86_64-dev.tar.gz’ in the folder pub/dist/freesurfer/dev/‘ but I’m not sure if this contains the third party dependencies and did not want to download without knowing. I do not have build-stamp.txt file in my $FREESURFER_HOME to provide you with the freesurfer version, but I am using the current version on the github repo (although that shouldn’t matter for this issue). Do you have any advice? I couldn’t find any similar issues in the archives, and the wiki says it was last updated this past September, so I believe it is still a current wiki. Thank you! Christian McDaniel ___________________________________________ Christian McDaniel President, Deep Learning @ UGA Data Scientist, UGA CVIOG ITOS Data Analytics Team Master’s Student, Institute for Artificial Intelligence Boyd GSRC University of Georgia Athens, GA

1 0

Pediatric longitudinal pipeline
by Stoyell, Sally Morgan 30 Oct '18

30 Oct '18

Hi all, We are looking at analyzing cortical thickness across time in a group of children. Ages are 6-16 and children each have one followup visit, between 1-3 years from first visit. We first ran the cross-sectional pipeline and analyzed change that way before coming across the longitudinal pipeline. The longitudinal pipeline finished without errors and both cross sectional and longitudinal surfaces seem good at first pass. When comparing the results (change in cortical thickness from first to second timepoint), there are large differences from the cross-sectional to the longitudinal processing in some, but not all of the subjects. The differences in the change of the cortical thickness range from 0.005 all the way up to a difference of 0.04, a difference between processing streams that's as big as the greatest difference in cortical thickness seen within a subject. Some participants switch from a positive to negative difference (i.e. now showing cortical thinning rather than thickening as the cross sectional indicated). Additionally, most of these participants show a greater change with the longitudinal pipeline, which makes us concerned that head size changes are influencing the results. What would be causing such differences between processing streams? Our conclusions from our data will differ slightly depending on which pipeline we use. Other questions and answers from the Freesurfer mail archive seem to indicate that if the pipeline worked it should be fine. Since it seems to work in our case should we just assume the longitudinal did better, or is there a reason we should be concerned that head growth from pediatric participants might have biased the longitudinal pipeline and caused these differences even though it seems to have run correctly? We weren't expecting the magnitude of differences we saw with the longitudinal pipeline, so we want to make sure before moving forward. Thanks, Sally Sally Stoyell Clinical Research Coordinator Department of Neurology Massachusetts General Hospital sstoyell(a)mgh.harvard.edu<mailto:sstoyell@mgh.harvard.edu> M: 607-280-9614

1 0

Getting the volume of a ?h.pial-outer-smoothed file
by Riccardo Falsini 30 Oct '18

30 Oct '18

External Email - Use Caution Dear Freesurfer experts, Hello, I am a student currently working in Frank Guenther's lab at Boston University. I am quite new to freesurfer, so forgive me if the following question may be elementary. I am interested in using freesurfer to compare the level of atrophy (preferably for different brain areas) in an individual subject to several controls. I'm wondering if there is any way to determine the volume of the '?h.pial-outer-smoothed', and corresponding '?h.pial' file generated from running the 'recon-all -s <subj> -localGI' command. The idea is that I could generate a metric representing a general level of atrophy in subjects by comparing these two volumes (or by comparing the '?h.pial-outer-smoothed' to intracranial volume), however, I have been unable to find a way to retrieve these values. Does anyone have any suggestions? I would greatly appreciate any help in this regard. Thank you for your help! Best, Riccardo Falsini

2 2

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