Freesurfer September 2021

freesurfer@nmr.mgh.harvard.edu

76 participants
107 discussions

Update FS version and manually edited controls
by Funk, Quentin 15 Sep '21

15 Sep '21

External Email - Use Caution Freesurfer experts, I have a collection of older controls that I have reconstructed with FS 5.3. Due to age, many of these controls have hypointensities in the white matter that led to some errors in reconstruction that needed to be manually fixed. Our new pipeline involves FS 6 (and soon 7, probably), and I'd like to be able to use this same group of controls aginst subjects who will be processed with newer versions of FS. Is there a way to do this that doesn't involve manually correcting the WM masks for each subject again? My naive idea would be to copy over the (edited) wm.mgz files from the old reconstructions into the new reconstruction folders, then re-do the new reconstructions, but I wanted to make sure that wouldn't break anything / wasn't unwise for reasons that I am sure to be not seeing. Thank you for any insight! Quentin Funk, PhD Houston Methodist Academic Institute 713-363-9003<tel:713-363-9003> Houston Methodist. Leading Medicine. U.S. News & World Report has named Houston Methodist Hospital the Best Hospital in Texas for 10 years in a row. Houston Methodist is the No. 1 hospital in Texas and No. 16 in the nation. For more than 100 years, Houston Methodist has provided the best — and safest — clinical care, advanced technology and patient experience. That is our promise of leading medicine. houstonmethodist.org twitter.com/MethodistHosp facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Postdoctoral Fellow Position in Simultaneous Spinal Cord-Brain fMRI
by Abdou Thiam 15 Sep '21

15 Sep '21

External Email - Use Caution DESCRIPTION The Systems Neuroscience & Pain Laboratory at Stanford University (SNAPL) is actively recruiting a postdoctoral fellow who will join our research project on chronic pain. Funded by the National Institute of Health and directed by neuroscience professors Sean Mackey and Gary Glover, our goal is to investigate mechanisms of chronic pain using methods we developed to image the entire CNS via simultaneous spinal cord/brain fMRI. Our plan is to characterize neurobiological mechanisms underlying chronic pain and use this information to develop objective biomarkers of pain, ultimately, to derive new personalized interventions. Given abundant findings that fMRI of the brain can act as biomarker for chronic pain conditions, we propose utilization of our simultaneous spinal cord/brain fMRI to develop biomarkers of pain severity. Our research can be categorized as follows: 1. CNS mechanisms of chronic pain and pain modulation, 2. central sensitization and descending modulation, 3. corticospinal biomarkers of chronic pain conditions, 4. predictive models of pain resilience. When you join, you will have opportunity to collaborate with top neuroscientists, psychologists, machine learning experts and pain specialists at Stanford. Additionally, you will have access to cutting-edge fMRI technology; to invent and develop your own related research. Multidisciplinary aspects of this project will allow you to explore diverse chronic pain topics ranging from biomarker design for degenerative conditions to heart rate variability as a simple biomarker for psychological disorders. We have a strong track record for successfully transitioning postdoctoral fellows to independent grant funding and faculty positions. We can offer NIH T32 training to select candidates. The ideal candidate is a motivated problem solver and innovator who has a neuroscience background, enjoys challenging the paradigms of contemporary research and experimentation, is proficient with computer-aided analysis, and is enthusiastic and passionate about fMRI acquisition. RESEARCH AREA * fMRI and behavioral data from Healthy Control and Fibromyalgia, * Novel analysis techniques for multiecho cardiac-gated fMRI, spinal cord/brain task/resting-state fMRI, * Experiment design for * temporal summation & central sensitization of pain, * conditioned pain modulation, * descending pain modulation & emotional reappraisal of pain, * Multivariate pattern analysis of spinal cord/brain data for corticospinal biomarker, * Simultaneous spinal cord/brain fMRI for multiple sclerosis, spinal cord injury & trauma, motor neuron disease. QUALIFICATION Applicants must have received, as of the beginning date of the appointment, an MD/PhD, MD or PhD or comparable doctoral degree from an accredited domestic or foreign institution. Experience in neuroimaging analysis is a must. Additional experience in any of these is a plus: 1. Cognitive / Affective Neuroscience 2. Computational modeling / Machine Learning / Neural Networks / ICA 3. Chronic pain 4. MATLAB / Python / R / Linux / C 5. SPM / AFNI / FSL / fMRIPrep APPLICATION MATERIALS Submit (1) CV, (2) NIH Biosketch, (3) Letter of Research Intent Find instructions, blank format pages, and sample biosketches here:<https://secure-web.cisco.com/1Gw3cKdrJJ5YO-Xix239BEzVR8sGJvGRaGxNslDo_fwSoT…> https://secure-web.cisco.com/1Gw3cKdrJJ5YO-Xix239BEzVR8sGJvGRaGxNslDo_fwSoT…. Applicants follow non-fellowship templates. Letter of Intent template is available<http://secure-web.cisco.com/1GyGUEJlHt71LAew-d0oQUp36d1ghRzSTzWAC4ce5DG0qQc…>here: http://secure-web.cisco.com/1GyGUEJlHt71LAew-d0oQUp36d1ghRzSTzWAC4ce5DG0qQc…. For more information, visit http://secure-web.cisco.com/1v2JVB1UtaPVopImV9dKbvKiLzxrwzYcPbEQKLn3KchLpMj… Address Letter of Research Intent to Christine Sze Wan Law: cslaw(a)stanford.edu<mailto:cslaw@stanford.edu>

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running freeview on MacOS Big Sur, version 11.5.2
by Jingyi Wang 14 Sep '21

14 Sep '21

External Email - Use Caution Dear freesurfer experts, I have a MacOS Big Sur, version 11.5.2 with an Intel chip. I successfully installed freesurfer on my computer. Unfortunately, the freeview quit unexpectedly every time I tried to open any file. Is the MacOS version 11.5.2 not supporting freeview? How can I solve this problem? Any insights can help! Thanks! Ps: I have attached the error message below, if needed.

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Freesurfer 7.1.0 VirtualBox password
by Camila Fernandes da Silva 14 Sep '21

14 Sep '21

External Email - Use Caution Dear admin, I instaled Freesurfer 7.1.0 using the VirtualBox in my Windows 10. It does not allow me to use it, It asks the developer password. Could you please help me? Thank you so much! -- Atenciosamente, Camila Fernandes Licenciatura em Física - IFUSP

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Job: MRI research associate, University of Delaware
by Keith Schneider 13 Sep '21

13 Sep '21

External Email - Use Caution Research Associate I, Research Office Pay Grade: 28N Context of the job: The Center for Biomedical and Brain Imaging (CBBI, cbbi.udel.edu) at the University of Delaware is hiring a research associate. The CBBI houses a research dedicated Siemens Prisma 3T MRI scanner and a Bruker 9.4T small bore MRI scanner, as well as TMS and EEG systems compatible with the MRI scanner. We are looking for a new member of our growing team. The CBBI is a university core facility that serves over 20 faculty from throughout the university. Under the general direction of the Center Manager, this position is responsible for supporting the general operation of the facility, including operating MRI scanners, completing various Quality Assurance tasks, and providing technical and operational support to users and CBBI staff. The Research Associate I will be expected to provide onsite coverage and support during evenings and weekends, periodically. Major Responsibilities: • Uses training and independent judgment to execute day-to-day activities, procedures, and research studies, ensuring efficient workflow, and adequate care and treatment of research participants and materials. • Ensures that established Quality Assurance initiatives are followed and documented appropriately. • Provides general operational support to users and CBBI personnel, including evenings and weekends, as needed, and coordinates with CBBI staff as necessary for vacation coverage and sick leave. • As needed, will provide operation of the Siemens Prisma 3T MRI and Bruker 9.4T scanner in compliance with the standard operating procedures of the CBBI, maintains a Level 2 safety certification within the CBBI, screens MRI subjects for safety, and assists CBBI researchers with exam-related tasks. • Assists in the use and maintenance of CBBI computers, databases, and peripheral equipment. • Adheres to appropriate data collection systems and procedures, according to pre-established research protocol; coordinates and monitors the collection and recording of data, as required by established study protocol. Maintains compliance to human and animal subject protocols. • Restocks center supplies and linens. • Accepts deliveries and notifies researchers of subject arrival, when appropriate. • Performs miscellaneous job-related duties as assigned. Qualifications: • Bachelor’s degree in neuroscience, psychology, radiology, radiologic technology, healthcare or other related fields. • Must be able to safely work around animals and strong magnetic fields. • Ability to follow research methodology and protocol. • Dependable, reliable, and able to consistently adhere to a schedule. • Ability to work independently. • Strong communication and interpersonal skills. • Ability to work collaboratively in a team environment. • Demonstrates an understanding and consideration of the differing needs and concerns of individuals with varying identities, cultures, and backgrounds. • Committed to fostering a workplace culture of belonging, where diversity is celebrated and equity is a core value. To apply, visit https://secure-web.cisco.com/1lttHPC-DOD5U1wYDMlTAEeIM80FPOG46eLoxuusT6vbn7… <https://secure-web.cisco.com/1lttHPC-DOD5U1wYDMlTAEeIM80FPOG46eLoxuusT6vbn7…> For more information, e-mail Trevor Wigal, CBBI Manager, twigal(a)udel.edu

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SAMSEG estimation error
by achille.teillac＠chu-lyon.fr 13 Sep '21

13 Sep '21

External Email - Use Caution Dear Stefano, Sorry for the delayed answer and thank you for your advice. As you mentionned, it was probably a template registration issue because when I updated my FS version to the 7.2, the cropping of 3D T1 and T2 FLAIR images stopped and the segmentation performed really well. Another concern I have is about the segmentation of the white matter hyperintensities (in the T2 FLAIR). It seems that SAMSEG does not succeed in finding the < small > lesions located in the most superior part of the brain. Do you have any feedback on that ? Best, Achille

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freeview: sh: 1: Syntax error: Bad fd number
by Peled, Noam 10 Sep '21

10 Sep '21

Hello! I'm trying to use freeview to visualize FSPGR dicoms files. I'm using ubuntu 18.04 with tcsh shell. I'm getting the following error: sh: 1: Syntax error: Bad fd number Here is the full error message: Starting DICOMRead2() dcmfile =~/Desktop/04254335/05641194 dcmdir = ~/Desktop/04254335 Ref Series No = 3 Found 200 files, checking for dicoms Found 200 files, checking for dicoms 5 /05641194 Found 198 dicom files in series. Found 198 dicom files in series. oms 5 /05641194 First Sorting Computing Slice Direction Vs: 0 0 1 Vs: 0 0 1 Second Sorting IsDWI = 0, IsPhilipsDWI = 0 Counting frames nframes = 1 nslices = 198 ndcmfiles = 198 INFO: rescale not needed PE Dir = ROW (dicom read) Loading pixel data JPEG compressed, decompressing cd ~/Desktop fsdcmdecompress --i ~/Desktop/04254335/05641194 --o /tmp/basuia.tmp.decompressed.dcm.yK9HZZ --jpeg >& /tmp/basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg.out sh: 1: Syntax error: Bad fd number ERROR: 512, see /tmp/basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg.out for more details QObject::~QObject: Timers cannot be stopped from another thread Thanks, Noam

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Matlab on macos big sur
by Szulia Agata 10 Sep '21

10 Sep '21

External Email - Use Caution Starting new thread as suggested by Douglas N. Greve: Hi, I’m using macos big sur 11.5.2, fs 7.2.0. I need volume estimations of hippocampal subfields, and so installed matlab in fs to have them collected. When I run the command "segmentHA_T1.sh”, matlab exits because of fatal error. I attach the crash report and the log file. Does anyone of you know how to successfully run matlab on mac? Kind regards, Agata Szulia Klauzula poufności. Ta wiadomość pocztowa i wszelkie załączone do niej pliki są poufne i podlegają ochronie prawnej. Jeśli nie jesteś jej prawidłowym adresatem, jakiekolwiek wykorzystanie w tym zapoznanie się z treścią przesłanych informacji, jej ujawnienie, reprodukcja, dystrybucja lub inne rozpowszechnienie, są ściśle zabronione. Jeśli otrzymał/a Pan/i niniejszy przekaz wskutek błędu, proszę o niezwłocznie powiadomienie nadawcy i usunięcie otrzymanych informacji. Kontakt: Uniwersytet Medyczny w Łodzi, 90–419 Łódź, Al. Kościuszki 4, Rektorat – Centrala, Tel. 42 272 59 66 umed.lodz.pl Confidentiality Notice - This e-mail is confidential, may be legally privileged. If you are not the intended recipient, you may not use, disclosure, distribute, copy, print or rely on this e-mail. If you received this e-mail in error, please notify the sender and delete the material from any computer.Contact:Medical University of Lodz, 90–419 Lodz, POLAND, 4 Kosciuszki Avenue, Rector’s Office, phone 0048 42 272 59 66 umed.lodz.pl

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Installation of freesurfer on local computer
by Jingyi Wang 10 Sep '21

10 Sep '21

External Email - Use Caution Hello freesurfer developers, I am attempting to use freeview to view the freesurfer output on my local computer (mac bigsur 11.5.2). Even though the installation went smoothly, the freeview failed to open any of my freesurfer volumetric or surface files. Everytime I open any of the files with freeview it is quite unexpected. Thank you in advance! Below are is the error reports: Process: freeview [885] Path: /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview Identifier: com.freesurfer.freeview Version: 0 Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: freeview [885] User ID: 501 Date/Time: 2021-09-09 22:41:35.740 -0700 OS Version: macOS 11.5.2 (20G95) Report Version: 12 Bridge OS Version: 5.5 (18P4759a) Anonymous UUID: 8EE85C99-41F0-D772-ED30-07F4515E40E8 Time Awake Since Boot: 220 seconds System Integrity Protection: enabled Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: EXC_I386_GPFLT Exception Note: EXC_CORPSE_NOTIFY Termination Signal: Segmentation fault: 11 Termination Reason: Namespace SIGNAL, Code 0xb Terminating Process: exc handler [885] Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 org.qt-project.QtGui 0x000000011c4ddbbe QPen::QPen() + 46 1 org.qt-project.QtGui 0x000000011c4afb15 QPainterState::QPainterState() + 69 2 org.qt-project.QtGui 0x000000011c485a01 QRasterPaintEngine::createState(QPainterState*) const + 49 3 org.qt-project.QtGui 0x000000011c49f978 QPainter::begin(QPaintDevice*) + 248 4 org.qt-project.QtGui 0x000000011c49f872 QPainter::QPainter(QPaintDevice*) + 242 5 libqcocoa.dylib 0x000000011ce789ce 0x11ce63000 + 88526 6 org.qt-project.QtGui 0x000000011c3edabf QBackingStore::beginPaint(QRegion const&) + 191 7 org.qt-project.QtWidgets 0x000000011bca5ebf 0x11bc88000 + 122559 8 org.qt-project.QtWidgets 0x000000011bcd48fd QWidget::event(QEvent*) + 1645 9 org.qt-project.QtWidgets 0x000000011bde5c45 QMainWindow::event(QEvent*) + 277 10 org.qt-project.QtWidgets 0x000000011bc9870d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 11 org.qt-project.QtWidgets 0x000000011bc99b12 QApplication::notify(QObject*, QEvent*) + 594 12 org.qt-project.QtCore 0x000000011c96f564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 13 org.qt-project.QtCore 0x000000011c97079e QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 878 14 libqcocoa.dylib 0x000000011ce98d39 0x11ce63000 + 220473 15 libqcocoa.dylib 0x000000011ce994a8 0x11ce63000 + 222376 16 com.apple.CoreFoundation 0x00007fff205db94c __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17 17 com.apple.CoreFoundation 0x00007fff205db8b4 __CFRunLoopDoSource0 + 180 18 com.apple.CoreFoundation 0x00007fff205db634 __CFRunLoopDoSources0 + 242 19 com.apple.CoreFoundation 0x00007fff205da05c __CFRunLoopRun + 893 20 com.apple.CoreFoundation 0x00007fff205d961c CFRunLoopRunSpecific + 563 21 com.apple.HIToolbox 0x00007fff2881fa83 RunCurrentEventLoopInMode + 292 22 com.apple.HIToolbox 0x00007fff2881f6b6 ReceiveNextEventCommon + 284 23 com.apple.HIToolbox 0x00007fff2881f583 _BlockUntilNextEventMatchingListInModeWithFilter + 70 24 com.apple.AppKit 0x00007fff22de1172 _DPSNextEvent + 864 25 com.apple.AppKit 0x00007fff22ddf945 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1364 26 com.apple.AppKit 0x00007fff22dd1c69 -[NSApplication run] + 586 27 libqcocoa.dylib 0x000000011ce98223 0x11ce63000 + 217635 28 org.qt-project.QtCore 0x000000011c96ab7f QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 431 29 org.qt-project.QtCore 0x000000011c96fb72 QCoreApplication::exec() + 130 30 com.freesurfer.freeview 0x000000010b2b07dd 0x10b1b0000 + 1050589 31 libdyld.dylib 0x00007fff204fdf3d start + 1 Thread 1: 0 libsystem_pthread.dylib 0x00007fff204de420 start_wqthread + 0 Thread 2: 0 libsystem_pthread.dylib 0x00007fff204de420 start_wqthread + 0 Thread 3: 0 libsystem_pthread.dylib 0x00007fff204de420 start_wqthread + 0 Thread 4: 0 libsystem_pthread.dylib 0x00007fff204de420 start_wqthread + 0 Thread 5:: QThread 0 libsystem_kernel.dylib 0x00007fff204b39ca poll + 10 1 org.qt-project.QtCore 0x000000011c9c58d0 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 608 2 org.qt-project.QtCore 0x000000011c9c70c7 QEventDispatcherUNIX::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 903 3 org.qt-project.QtCore 0x000000011c96ab7f QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 431 4 org.qt-project.QtCore 0x000000011c7a637c QThread::exec() + 140 5 org.qt-project.QtCore 0x000000011c7a72f3 0x11c785000 + 140019 6 libsystem_pthread.dylib 0x00007fff204e28fc _pthread_start + 224 7 libsystem_pthread.dylib 0x00007fff204de443 thread_start + 15 Thread 6:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x00007fff204ad2ba mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff204ad62c mach_msg + 60 2 com.apple.CoreFoundation 0x00007fff205dbb2f __CFRunLoopServiceMachPort + 316 3 com.apple.CoreFoundation 0x00007fff205da20f __CFRunLoopRun + 1328 4 com.apple.CoreFoundation 0x00007fff205d961c CFRunLoopRunSpecific + 563 5 com.apple.AppKit 0x00007fff22f6723a _NSEventThread + 124 6 libsystem_pthread.dylib 0x00007fff204e28fc _pthread_start + 224 7 libsystem_pthread.dylib 0x00007fff204de443 thread_start + 15 Thread 7: 0 libsystem_pthread.dylib 0x00007fff204de420 start_wqthread + 0 Thread 8: 0 libsystem_pthread.dylib 0x00007fff204de420 start_wqthread + 0 Thread 9: 0 libsystem_pthread.dylib 0x00007fff204de420 start_wqthread + 0 Thread 10:: ThreadIOWorker 0 org.qt-project.QtCore 0x000000011ca434a1 0x11c785000 + 2876577 1 org.qt-project.QtCore 0x000000011c801e69 QHashData::free_helper(void (*)(QHashData::Node*)) + 73 2 org.qt-project.QtCore 0x000000011ca48b2d 0x11c785000 + 2898733 3 org.qt-project.QtCore 0x000000011ca47089 0x11c785000 + 2891913 4 org.qt-project.QtCore 0x000000011ca4717e 0x11c785000 + 2892158 5 org.qt-project.QtCore 0x000000011ca368ce 0x11c785000 + 2824398 6 org.qt-project.QtCore 0x000000011ca3aeda 0x11c785000 + 2842330 7 libsystem_c.dylib 0x00007fff20411d25 __cxa_finalize_ranges + 316 8 libsystem_c.dylib 0x00007fff20412010 exit + 53 9 com.freesurfer.freeview 0x000000010c42787c 0x10b1b0000 + 19363964 10 com.freesurfer.freeview 0x000000010c4b04f8 0x10b1b0000 + 19924216 11 com.freesurfer.freeview 0x000000010b224f2c 0x10b1b0000 + 479020 12 com.freesurfer.freeview 0x000000010b2255bd 0x10b1b0000 + 480701 13 com.freesurfer.freeview 0x000000010b24ccc5 0x10b1b0000 + 642245 14 com.freesurfer.freeview 0x000000010b3370af 0x10b1b0000 + 1601711 15 org.qt-project.QtCore 0x000000011c7a72f3 0x11c785000 + 140019 16 libsystem_pthread.dylib 0x00007fff204e28fc _pthread_start + 224 17 libsystem_pthread.dylib 0x00007fff204de443 thread_start + 15 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000d5511dc36a10 rbx: 0x00007fb0dd812e40 rcx: 0x0000000000000001 rdx: 0x00007fb0dd812e00 rdi: 0x00007fb0dd812e40 rsi: 0x0000600001db8d10 rbp: 0x00007ffee4a4bf40 rsp: 0x00007ffee4a4bf10 r8: 0x00000000000018d4 r9: 0x00007fb0dd808101 r10: 0x0000000000003f01 r11: 0x00007fb0dd800000 r12: 0x0000000000000000 r13: 0x00006000024d0dd0 r14: 0x0000000000000000 r15: 0x00007ffee4a4c0a0 rip: 0x000000011c4ddbbe rfl: 0x0000000000010282 cr2: 0x00007fb0de809df0 Logical CPU: 2 Error Code: 0x00000000 Trap Number: 13 Thread 0 instruction stream: 00 00 55 48 89 e5 8b 47-08 48 c7 06 00 00 00 00 ..UH...G.H...... 89 46 08 8b 47 0c 89 46-0c 8b 47 10 89 46 10 5d .F..G..F..G..F.] c3 90 55 48 89 e5 5d c3-90 90 90 90 90 90 90 90 ..UH..]......... 90 90 55 48 89 e5 41 57-41 56 41 55 41 54 53 50 ..UH..AWAVAUATSP 48 89 fb 8b 05 99 68 1c-00 8b 05 93 68 1c 00 85 H.....h.....h... c0 79 1f 48 8b 05 48 68-1c 00 48 8b 00 48 89 03 .y.H..Hh..H..H.. [f0]ff 00 48 83 c4 08 5b-41 5c 41 5d 41 5e 41 5f ...H...[A\A]A^A_ <== 5d c3 4c 8d 35 31 68 1c-00 4c 89 f7 e8 99 a8 14 ].L.51h..L...... 00 8b 05 5b 68 1c 00 85-c0 0f 85 c3 00 00 00 bf ...[h........... 08 00 00 00 e8 8d b4 14-00 49 89 c7 48 8d 7d d0 .........I..H.}. be 02 00 00 00 ba 01 00-00 00 e8 f3 5c f2 ff bf ............\... 48 00 00 00 e8 6d b4 14-00 49 89 c5 41 c7 45 00 H....m...I..A.E. Thread 0 last branch register state not available. 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0x7fff6bc13fff libGLImage.dylib (18.5.9) <2CCBC785-6F45-33DE-B790-066AF4C69048> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib 0x7fff6bc14000 - 0x7fff6bc50fff libGLU.dylib (18.5.9) <53602650-F093-334F-9D96-2B4FE2359E7A> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib 0x7fff6bc51000 - 0x7fff6bde4fff libGLProgrammability.dylib (18.5.9) <A85B6455-FB77-3E5E-AD6C-27543EDC4415> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib 0x7fff6bde5000 - 0x7fff6bdeffff libGL.dylib (18.5.9) <9E1A856D-D393-3FDC-ABDF-E29282A6B83E> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib 0x7fff6bdf0000 - 0x7fff6bf6dfff GLEngine (18.5.9) <42EA70F3-CD0B-3C41-8A78-90AEE7CB0F96> /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine 0x7fff6bf6e000 - 0x7fff6bf96fff GLRendererFloat (18.5.9) <4953ACAF-885A-310A-BFDF-777C9627CCDE> /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat 0x7fff6d22f000 - 0x7fff6d287fff com.apple.opencl (4.6 - 4.6) <5FD1A8D9-17B9-316B-8CA4-6BE553B936CE> /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL 0x7fff6e331000 - 0x7fff6e338fff com.apple.agl (3.3.4 - AGL-3.3.3) <C7C621A8-A60D-3486-A4E6-74A1D696A369> /System/Library/Frameworks/AGL.framework/Versions/A/AGL 0x7fff77a63000 - 0x7fff77a6afff libRosetta.dylib (203.58) <A7FFAFB5-B0AB-312E-8EB6-FAF56D76FB7D> /usr/lib/libRosetta.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by all processes on this machine: task_for_pid: 0 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=802.8M resident=0K(0%) swapped_out_or_unallocated=802.8M(100%) Writable regions: Total=1.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.0G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 1024K 8 Activity Tracing 256K 1 CG backing stores 4320K 12 CG image 3184K 16 CG raster data 2984K 1 CoreAnimation 68.9M 35 CoreGraphics 16K 3 CoreImage 40K 2 CoreUI image data 3256K 24 Foundation 16K 1 Kernel Alloc Once 8K 1 MALLOC 381.4M 108 MALLOC guard page 32K 7 MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated) STACK GUARD 56.0M 11 Stack 13.1M 11 VM_ALLOCATE 268K 35 __DATA 258.9M 364 __DATA_CONST 17.2M 200 __DATA_DIRTY 790K 119 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 504.4M 25 __OBJC_RO 70.2M 1 __OBJC_RW 2496K 3 __TEXT 298.4M 362 __UNICODE 588K 1 mapped file 231.0M 30 shared memory 788K 21 =========== ======= ======= TOTAL 2.3G 1405 TOTAL, minus reserved VM space 1.9G 1405 Model: MacBookPro16,2, BootROM 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0), 4 processors, Quad-Core Intel Core i7, 2.3 GHz, 16 GB, SMC Graphics: kHW_IntelIrisPlusGraphicsItem, Intel Iris Plus Graphics, spdisplays_builtin Memory Module: BANK 0/ChannelA-DIMM0, 8 GB, LPDDR4X, 3733 MHz, SK Hynix, - Memory Module: BANK 2/ChannelB-DIMM0, 8 GB, LPDDR4X, 3733 MHz, SK Hynix, - AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x7BF), wl0: Jul 7 2021 02:54:21 version 9.30.444.17.32.5.70 FWID 01-6551fb93 Bluetooth: Version 8.0.5d7, 3 services, 27 devices, 1 incoming serial ports Network Service: Wi-Fi, AirPort, en0 USB Device: USB 3.1 Bus USB Device: USB3.0 Hub USB Device: 4-Port USB 3.0 Hub USB Device: USB3.0 Card Reader USB Device: AX88179 USB Device: USB 3.1 Bus USB Device: USB2.0 Hub USB Device: 4-Port USB 2.0 Hub USB Device: 2.4G Wireless Receiver USB Device: Apple T2 Bus USB Device: Touch Bar Backlight USB Device: Touch Bar Display USB Device: Apple Internal Keyboard / Trackpad USB Device: Headset USB Device: Ambient Light Sensor USB Device: FaceTime HD Camera (Built-in) USB Device: Apple T2 Controller Thunderbolt Bus: MacBook Pro, Apple Inc., 85.0 Thunderbolt Bus: MacBook Pro, Apple Inc., 85.0Process: freeview [885] Path: /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview Identifier: com.freesurfer.freeview Version: 0 Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: freeview [885] User ID: 501 Date/Time: 2021-09-09 22:41:35.740 -0700 OS Version: macOS 11.5.2 (20G95) Report Version: 12 Bridge OS Version: 5.5 (18P4759a) Anonymous UUID: 8EE85C99-41F0-D772-ED30-07F4515E40E8 Time Awake Since Boot: 220 seconds System Integrity Protection: enabled Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: EXC_I386_GPFLT Exception Note: EXC_CORPSE_NOTIFY Termination Signal: Segmentation fault: 11 Termination Reason: Namespace SIGNAL, Code 0xb Terminating Process: exc handler [885] Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 org.qt-project.QtGui 0x000000011c4ddbbe QPen::QPen() + 46 1 org.qt-project.QtGui 0x000000011c4afb15 QPainterState::QPainterState() + 69 2 org.qt-project.QtGui 0x000000011c485a01 QRasterPaintEngine::createState(QPainterState*) const + 49 3 org.qt-project.QtGui 0x000000011c49f978 QPainter::begin(QPaintDevice*) + 248 4 org.qt-project.QtGui 0x000000011c49f872 QPainter::QPainter(QPaintDevice*) + 242 5 libqcocoa.dylib 0x000000011ce789ce 0x11ce63000 + 88526 6 org.qt-project.QtGui 0x000000011c3edabf QBackingStore::beginPaint(QRegion const&) + 191 7 org.qt-project.QtWidgets 0x000000011bca5ebf 0x11bc88000 + 122559 8 org.qt-project.QtWidgets 0x000000011bcd48fd QWidget::event(QEvent*) + 1645 9 org.qt-project.QtWidgets 0x000000011bde5c45 QMainWindow::event(QEvent*) + 277 10 org.qt-project.QtWidgets 0x000000011bc9870d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 11 org.qt-project.QtWidgets 0x000000011bc99b12 QApplication::notify(QObject*, QEvent*) + 594 12 org.qt-project.QtCore 0x000000011c96f564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 13 org.qt-project.QtCore 0x000000011c97079e QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 878 14 libqcocoa.dylib 0x000000011ce98d39 0x11ce63000 + 220473 15 libqcocoa.dylib 0x000000011ce994a8 0x11ce63000 + 222376 16 com.apple.CoreFoundation 0x00007fff205db94c __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17 17 com.apple.CoreFoundation 0x00007fff205db8b4 __CFRunLoopDoSource0 + 180 18 com.apple.CoreFoundation 0x00007fff205db634 __CFRunLoopDoSources0 + 242 19 com.apple.CoreFoundation 0x00007fff205da05c __CFRunLoopRun + 893 20 com.apple.CoreFoundation 0x00007fff205d961c CFRunLoopRunSpecific + 563 21 com.apple.HIToolbox 0x00007fff2881fa83 RunCurrentEventLoopInMode + 292 22 com.apple.HIToolbox 0x00007fff2881f6b6 ReceiveNextEventCommon + 284 23 com.apple.HIToolbox 0x00007fff2881f583 _BlockUntilNextEventMatchingListInModeWithFilter + 70 24 com.apple.AppKit 0x00007fff22de1172 _DPSNextEvent + 864 25 com.apple.AppKit 0x00007fff22ddf945 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1364 26 com.apple.AppKit 0x00007fff22dd1c69 -[NSApplication run] + 586 27 libqcocoa.dylib 0x000000011ce98223 0x11ce63000 + 217635 28 org.qt-project.QtCore 0x000000011c96ab7f QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 431 29 org.qt-project.QtCore 0x000000011c96fb72 QCoreApplication::exec() + 130 30 com.freesurfer.freeview 0x000000010b2b07dd 0x10b1b0000 + 1050589 31 libdyld.dylib 0x00007fff204fdf3d start + 1 Thread 1: 0 libsystem_pthread.dylib 0x00007fff204de420 start_wqthread + 0 Thread 2: 0 libsystem_pthread.dylib 0x00007fff204de420 start_wqthread + 0 Thread 3: 0 libsystem_pthread.dylib 0x00007fff204de420 start_wqthread + 0 Thread 4: 0 libsystem_pthread.dylib 0x00007fff204de420 start_wqthread + 0 Thread 5:: QThread 0 libsystem_kernel.dylib 0x00007fff204b39ca poll + 10 1 org.qt-project.QtCore 0x000000011c9c58d0 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 608 2 org.qt-project.QtCore 0x000000011c9c70c7 QEventDispatcherUNIX::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 903 3 org.qt-project.QtCore 0x000000011c96ab7f QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 431 4 org.qt-project.QtCore 0x000000011c7a637c QThread::exec() + 140 5 org.qt-project.QtCore 0x000000011c7a72f3 0x11c785000 + 140019 6 libsystem_pthread.dylib 0x00007fff204e28fc _pthread_start + 224 7 libsystem_pthread.dylib 0x00007fff204de443 thread_start + 15 Thread 6:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x00007fff204ad2ba mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff204ad62c mach_msg + 60 2 com.apple.CoreFoundation 0x00007fff205dbb2f __CFRunLoopServiceMachPort + 316 3 com.apple.CoreFoundation 0x00007fff205da20f __CFRunLoopRun + 1328 4 com.apple.CoreFoundation 0x00007fff205d961c CFRunLoopRunSpecific + 563 5 com.apple.AppKit 0x00007fff22f6723a _NSEventThread + 124 6 libsystem_pthread.dylib 0x00007fff204e28fc _pthread_start + 224 7 libsystem_pthread.dylib 0x00007fff204de443 thread_start + 15 Thread 7: 0 libsystem_pthread.dylib 0x00007fff204de420 start_wqthread + 0 Thread 8: 0 libsystem_pthread.dylib 0x00007fff204de420 start_wqthread + 0 Thread 9: 0 libsystem_pthread.dylib 0x00007fff204de420 start_wqthread + 0 Thread 10:: ThreadIOWorker 0 org.qt-project.QtCore 0x000000011ca434a1 0x11c785000 + 2876577 1 org.qt-project.QtCore 0x000000011c801e69 QHashData::free_helper(void (*)(QHashData::Node*)) + 73 2 org.qt-project.QtCore 0x000000011ca48b2d 0x11c785000 + 2898733 3 org.qt-project.QtCore 0x000000011ca47089 0x11c785000 + 2891913 4 org.qt-project.QtCore 0x000000011ca4717e 0x11c785000 + 2892158 5 org.qt-project.QtCore 0x000000011ca368ce 0x11c785000 + 2824398 6 org.qt-project.QtCore 0x000000011ca3aeda 0x11c785000 + 2842330 7 libsystem_c.dylib 0x00007fff20411d25 __cxa_finalize_ranges + 316 8 libsystem_c.dylib 0x00007fff20412010 exit + 53 9 com.freesurfer.freeview 0x000000010c42787c 0x10b1b0000 + 19363964 10 com.freesurfer.freeview 0x000000010c4b04f8 0x10b1b0000 + 19924216 11 com.freesurfer.freeview 0x000000010b224f2c 0x10b1b0000 + 479020 12 com.freesurfer.freeview 0x000000010b2255bd 0x10b1b0000 + 480701 13 com.freesurfer.freeview 0x000000010b24ccc5 0x10b1b0000 + 642245 14 com.freesurfer.freeview 0x000000010b3370af 0x10b1b0000 + 1601711 15 org.qt-project.QtCore 0x000000011c7a72f3 0x11c785000 + 140019 16 libsystem_pthread.dylib 0x00007fff204e28fc _pthread_start + 224 17 libsystem_pthread.dylib 0x00007fff204de443 thread_start + 15 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000d5511dc36a10 rbx: 0x00007fb0dd812e40 rcx: 0x0000000000000001 rdx: 0x00007fb0dd812e00 rdi: 0x00007fb0dd812e40 rsi: 0x0000600001db8d10 rbp: 0x00007ffee4a4bf40 rsp: 0x00007ffee4a4bf10 r8: 0x00000000000018d4 r9: 0x00007fb0dd808101 r10: 0x0000000000003f01 r11: 0x00007fb0dd800000 r12: 0x0000000000000000 r13: 0x00006000024d0dd0 r14: 0x0000000000000000 r15: 0x00007ffee4a4c0a0 rip: 0x000000011c4ddbbe rfl: 0x0000000000010282 cr2: 0x00007fb0de809df0 Logical CPU: 2 Error Code: 0x00000000 Trap Number: 13 Thread 0 instruction stream: 00 00 55 48 89 e5 8b 47-08 48 c7 06 00 00 00 00 ..UH...G.H...... 89 46 08 8b 47 0c 89 46-0c 8b 47 10 89 46 10 5d .F..G..F..G..F.] c3 90 55 48 89 e5 5d c3-90 90 90 90 90 90 90 90 ..UH..]......... 90 90 55 48 89 e5 41 57-41 56 41 55 41 54 53 50 ..UH..AWAVAUATSP 48 89 fb 8b 05 99 68 1c-00 8b 05 93 68 1c 00 85 H.....h.....h... c0 79 1f 48 8b 05 48 68-1c 00 48 8b 00 48 89 03 .y.H..Hh..H..H.. [f0]ff 00 48 83 c4 08 5b-41 5c 41 5d 41 5e 41 5f ...H...[A\A]A^A_ <== 5d c3 4c 8d 35 31 68 1c-00 4c 89 f7 e8 99 a8 14 ].L.51h..L...... 00 8b 05 5b 68 1c 00 85-c0 0f 85 c3 00 00 00 bf ...[h........... 08 00 00 00 e8 8d b4 14-00 49 89 c7 48 8d 7d d0 .........I..H.}. be 02 00 00 00 ba 01 00-00 00 e8 f3 5c f2 ff bf ............\... 48 00 00 00 e8 6d b4 14-00 49 89 c5 41 c7 45 00 H....m...I..A.E. Thread 0 last branch register state not available. 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0x7fff6d287fff com.apple.opencl (4.6 - 4.6) <5FD1A8D9-17B9-316B-8CA4-6BE553B936CE> /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL 0x7fff6e331000 - 0x7fff6e338fff com.apple.agl (3.3.4 - AGL-3.3.3) <C7C621A8-A60D-3486-A4E6-74A1D696A369> /System/Library/Frameworks/AGL.framework/Versions/A/AGL 0x7fff77a63000 - 0x7fff77a6afff libRosetta.dylib (203.58) <A7FFAFB5-B0AB-312E-8EB6-FAF56D76FB7D> /usr/lib/libRosetta.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by all processes on this machine: task_for_pid: 0 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=802.8M resident=0K(0%) swapped_out_or_unallocated=802.8M(100%) Writable regions: Total=1.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.0G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 1024K 8 Activity Tracing 256K 1 CG backing stores 4320K 12 CG image 3184K 16 CG raster data 2984K 1 CoreAnimation 68.9M 35 CoreGraphics 16K 3 CoreImage 40K 2 CoreUI image data 3256K 24 Foundation 16K 1 Kernel Alloc Once 8K 1 MALLOC 381.4M 108 MALLOC guard page 32K 7 MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated) STACK GUARD 56.0M 11 Stack 13.1M 11 VM_ALLOCATE 268K 35 __DATA 258.9M 364 __DATA_CONST 17.2M 200 __DATA_DIRTY 790K 119 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 504.4M 25 __OBJC_RO 70.2M 1 __OBJC_RW 2496K 3 __TEXT 298.4M 362 __UNICODE 588K 1 mapped file 231.0M 30 shared memory 788K 21 =========== ======= ======= TOTAL 2.3G 1405 TOTAL, minus reserved VM space 1.9G 1405 Model: MacBookPro16,2, BootROM 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0), 4 processors, Quad-Core Intel Core i7, 2.3 GHz, 16 GB, SMC Graphics: kHW_IntelIrisPlusGraphicsItem, Intel Iris Plus Graphics, spdisplays_builtin Memory Module: BANK 0/ChannelA-DIMM0, 8 GB, LPDDR4X, 3733 MHz, SK Hynix, - Memory Module: BANK 2/ChannelB-DIMM0, 8 GB, LPDDR4X, 3733 MHz, SK Hynix, - AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x7BF), wl0: Jul 7 2021 02:54:21 version 9.30.444.17.32.5.70 FWID 01-6551fb93 Bluetooth: Version 8.0.5d7, 3 services, 27 devices, 1 incoming serial ports Network Service: Wi-Fi, AirPort, en0 USB Device: USB 3.1 Bus USB Device: USB3.0 Hub USB Device: 4-Port USB 3.0 Hub USB Device: USB3.0 Card Reader USB Device: AX88179 USB Device: USB 3.1 Bus USB Device: USB2.0 Hub USB Device: 4-Port USB 2.0 Hub USB Device: 2.4G Wireless Receiver USB Device: Apple T2 Bus USB Device: Touch Bar Backlight USB Device: Touch Bar Display USB Device: Apple Internal Keyboard / Trackpad USB Device: Headset USB Device: Ambient Light Sensor USB Device: FaceTime HD Camera (Built-in) USB Device: Apple T2 Controller Thunderbolt Bus: MacBook Pro, Apple Inc., 85.0 Thunderbolt Bus: MacBook Pro, Apple Inc., 85.0

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Re: [Freesurfer] Password Ubuntu VM
by fsbuild 10 Sep '21

10 Sep '21

External Email - Use Caution Sending the info to your private email shortly. - R. On Sep 9, 2021, at 05:08, Daniel Chiaretti <danielchiaretti(a)gmail.com> wrote:        External Email - Use Caution        Dear Freesurfers,I am trying to set up the virtual box freesurfer. However, after starting up the virtual machine it is asking for a password for the 'developer' user. Which password should I use?Thanks in advance,Daniel_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer September 2021