Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30083 discussions

Converting .trk files in mini space to nifti using dorm_trk2trk
by Schaechter, Judith D. 23 Nov '21

23 Nov '21

Hi, I'd like to convert *trk files that are in mni space to nifti files using dmri_trk2trk. The *trk files are here: /autofs/vast/freesurfer/centos7_x86_64/7.2.0-beta/trctrain/hcp/mni Attempts so far (that have failed) are: dmri_trk2trk --in TRACK_FILE.display.trk --outvol TRACK_FILE.display.mni.nii.gz --inref ../MGH35_HCP_FA_template.nii.gz --outref ../MGH35_HCP_FA_template.nii.gz dmri_trk2trk --in TRACK_FILE.display.trk --outvol TRACK_FILE.display.mni.nii.gz --inref ../MGH35_HCP_FA_template.nii.gz --outref ../MGH35_HCP_FA_template.nii.gz --reg MGH35_HCP_FA_template_identity.mat with MGH35_HCP_FA_template_identity.mat generated by: flirt -in MGH35_HCP_FA_template.nii.gz -ref MGH35_HCP_FA_template.nii.gz -omat MGH35_HCP_FA_template_identity.mat dmri_trk2trk --in TRACK_FILE.display.trk --outvol TRACK_FILE.display.mni.nii.gz --inref ../MGH35_HCP_FA_template.nii.gz --outref ../MGH35_HCP_FA_template.nii.gz --reg MGH35_HCP_FA_2_MNI152_T1_2mm_brain.mat with MGH35_HCP_FA_2_MNI152_T1_2mm_brain.mat generated by: flirt -in MGH35_HCP_FA_template.nii.gz -ref MNI152_T1_2mm_brain.nii.gz -omat MGH35_HCP_FA_2_MNI152_T1_2mm_brain.mat Thanks in advance for your help! Judith ******************************************************* Judith D. Schaechter, Ph.D., M.S.P.T. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital, Harvard Medical School 13th Street, Building 149, Room 2301 Charlestown, MA 02129 Office 617-726-5622 | Cell 781-752-6247 | Fax 617-726-7422 Email jschaechter(a)mgh.harvard.edu

2 3

Freeview grey matter, white matter and Tracula outputs
by Zeng, Qi 23 Nov '21

23 Nov '21

External Email - Use Caution Hi, If I want to freeview fully segmented grey matter, white matter, and Tracula outputs, are the following commands correct to the request? # to visualize the segmented cortical outputs freeview -v mri/aparc+aseg.mgz Question: why is one hemisphere brighter than the other? How can I adjust so that they are equally bright? # to visualize the segmented subcortical outputs freeview -v mri/aseg.mgz Question: why is only one hemisphere showing and how to add the other one? $ to visualize AD. RD, FA and color-coded each freeview -v dmri/dtifit_FA.nii Question: I cannot find the nifti outputs of AD and RD (however, the stats generated). where can I find it? Is there an example of how to color-code them for freeview? Thank you! Best, Jackie

2 3

[WARNING: ATTACHMENT UNSCANNED]Using a Different Atlas for Anatomical ROI Analysis
by Flanagan, Shawn D 23 Nov '21

23 Nov '21

External Email - Use Caution Hello, I would like to use the Brainnectome atlas for cortical thickness analysis parcellations. The T1 template volume (nifti file type) is attached if helpful. I have seen a couple of posts on this, but am not clear about the process. For example, the response to a similar comment was to “run recon-all on the AAL anatomical T1w volume template”. At this point, I do not know what files, transformations, and/or code modifications are needed. For example, does the brainnectome template volume need to be preprocessed in any way, does it need to be saved in the MGH format? If so, how is this done? Does the process require any other files or subroutines? In summary, I am wondering if you can “walk me through” the process or provide a detailed example. Any help would be greatly appreciated! Thank you for your time. Best, Shawn --- Shawn Flanagan, Ph.D. Assistant Professor University of Pittsburgh School of Health and Rehabilitation Sciences Department of Sports Medicine and Nutrition Neuromuscular Research Laboratory Warrior Human Performance Research Center 3860 South Water Street Pittsburgh, PA 15203 sdf29(a)pitt.edu<mailto:sdf29@pitt.edu> Email 412.246.0460 Office 630.854.0547 Mobile Neuromuscular Research Laboratory<http://secure-web.cisco.com/1w-f2b1Sv8FoWJqjWBtRI_gzdJ3kwmFPg5ehq75ANa6Is4a…>

2 2

Pipeline errors - matlab
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 22 Nov '21

22 Nov '21

External Email - Use Caution Hello Freesurfer experts! Hope that you are all well. I am having errors when running hippocampal subfields and thalamic subfields. When in the error log for the hippocampal pipeline, this is part of the error that I got: *MATLAB is exiting because of fatal error* */Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 37: 7498 Killed: 9 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args* *Darwin CCAPSY-0GYM0XV 20.6.0 Darwin Kernel Version 20.6.0: Mon Aug 30 06:12:21 PDT 2021; root:xnu-7195.141.6~3/RELEASE_X86_64 x86_64* *T1 hippocampal subfields exited with ERRORS at Fri Nov 12 14:26:43 EST 2021* Please let me know if additional info is needed. Thank you so much, Alex

2 3

Postdoctoral Positions in Clinical and Contemplative Neuroscience at McLean Hospital/Harvard Medical School
by Margiotta, Kathryn Nicole 22 Nov '21

22 Nov '21

[cid:ffcafe71-529c-423a-8564-7c00e4b3ff4d] Postdoctoral Positions in Clinical and Contemplative Neuroscience at McLean Hospital/Harvard Medical School Postdoctoral positions are available under the mentorship of Dr. Matthew D. Sacchet within the Meditation Research Group of the Center for Depression, Anxiety, and Stress Research at McLean Hospital/Harvard Medical School. These positions are fully supported by NIH and Foundation funds. The Meditation Research Group (Directed by Dr. Sacchet; https://meditation.mclean.harvard.edu/) advances the science of meditation in both clinical and non-clinical contexts and the neuroscience of depression. The Group’s studies span and integrate affective and cognitive neuroscience, clinical psychology and psychiatry, computer science and related computational disciplines, contemplative and religious studies, neuro- and micro-phenomenology, human neuroimaging, and psychoneuroimmunology including epigenetics and stress physiology. The Center for Depression, Anxiety and Stress Research (CDASR; Directed by Dr. Diego A. Pizzagalli; http://cdasr.mclean.harvard.edu<http://cdasr.mclean.harvard.edu/>) is a vibrant research center with over 40 scientists/staff/students that embraces a multi-disciplinary approach to improve our understanding of the psychological, environmental, and neurobiological factors associated with depression, anxiety, and related disorders across the lifespan. Successful candidates will be expected to lead and collaborate on projects that advance one or both of the neuroscience of depression and/or the neuroscience of meditation. The candidate will have access to extensive existing and newly acquired data across these two domains. Opportunities will be available to pursue independent research and interdisciplinary collaborations across Harvard Medical School and beyond. Depending on research focus, candidates will have access to research-dedicated human MRI scanners (3T, 4T, and 7T) as well as two high-density EEG systems. Qualifications: A strong background in functional MRI analysis is required. Expertise in clinical neuroscience or contemplative neuroscience is desired though not required. Additional experience with a second imaging modality (notably EEG) and in computational approaches (e.g., computational modeling, machine learning) will also be considered. To apply, send a CV, a cover letter describing research interests, as well as names and email addresses of three references to Matthew D. Sacchet (msacchet(a)mclean.harvard.edu<mailto:msacchet@mclean.harvard.edu>). Review of applications will begin immediately (expected start date: early 2022, although other timeframes may be possible). About McLean Hospital and Harvard Medical School Since 1811, McLean Hospital has been a world leader in scientific investigations and treatments of mental illnesses as well as in training generations of scientists and clinicians. McLean Hospital is the flagship psychiatric affiliate and teaching hospital of Harvard Medical School. McLean Hospital maintains the largest program of research in neuroscience and psychiatry of any private psychiatric hospital in the United States. McLean Hospital has been ranked as America’s best freestanding psychiatric hospital for 18 consecutive years by U.S. News and World Report. U.S. News and World Report has consistently ranked Harvard Medical School as the best Research Medical School with the best Psychiatry Program. McLean Hospital is in Belmont, Massachusetts, approximately 5 miles from Boston. McLean Hospital is located in Belmont, Massachusetts, approximately 5 miles from Boston. McLean Hospital, which is an affiliate of Harvard Medical School, is an Equal Opportunity Employer. As an equal opportunity employer, McLean seeks qualified candidates for all posted employment opportunities without regard to race, color, age, religion, gender, national origin, disability or veteran status. McLean particularly welcomes applications from minorities, women, and persons with disabilities.

1 0

PhD Position Available @ University of Delaware: Movement Disorders/Parkinson's Disease Research
by Roxana Burciu 22 Nov '21

22 Nov '21

External Email - Use Caution The Motor Neuroscience and Neuroimaging Laboratory in the Department of Kinesiology and Applied Physiology at the University of Delaware ( https://secure-web.cisco.com/1FGUBbOfcKBczlqb5RsAtMzP59F-DjBkVa-NfDgzN_TBY1…) led by Dr. Roxana Burciu, is seeking motivated and enthusiastic students interested in pursuing a PhD in Neuroscience starting in Fall 2022. The lab aims to improve our understanding of human neural control of movement and leverage this information to improve motor function, mobility and the quality of life of individuals with movement disorders such as Parkinson’s disease. Students will work in an innovative research program that combines advanced functional and structural brain MRI techniques (task-based and resting state fMRI, arterial spin labelling, diffusion MRI, SWI), behavioral protocols and genetics to understand how the brain and behavior change in people with Parkinson’s disease and those at risk of developing the disease. The lab has access to UD’s Center for Biomedical and Brain Imaging which houses a 3T Siemens Magnetom Prisma whole-body MRI scanner and a 9.4 Bruker Biospec 94/20, designed for pre-clinical MR imaging and MRI research. The lab is also integrated with several other research laboratories studying the neural control of movement in healthy and Parkinson’s disease, which provides a rich scientific and collaborative community. PhD positions are funded through a combination of teaching and research assistantships. Requirements: - Have a background in neuroscience, biomedical engineering, kinesiology, psychology, or biomedical sciences. - Previous MRI experience is desirable. Have some experience with signal processing, bash, MATLAB or similar programming languages. - Be team-minded, flexible with the required tact and sensitivity for working with patients with neurological disorders. Potential applicants should contact Dr. Roxana Burciu at rgburciu(a)udel.edu with a brief email expressing their research interests, and a current CV. -- *Roxana G. Burciu, Ph.D. | **Assistant Professor* Department of Kinesiology and Applied Physiology, University of Delaware 347 STAR Tower, 100 Discovery Blvd., Newark DE, 19713 E: rgburciu(a)udel.edu | T: (302)-831-3066 | F: (302)-831-8813 Motor Neuroscience and Neuroimaging Lab: https://secure-web.cisco.com/1FGUBbOfcKBczlqb5RsAtMzP59F-DjBkVa-NfDgzN_TBY1… <https://secure-web.cisco.com/1w_QDOJZ2yFKkxLhwU9QrysW0rqX5hzSItrB2IEzWHNvfa…>

1 0

Postdoctoral position in Developmental/Affective/Clinical Neuroscience
by Jeffrey Spielberg 22 Nov '21

22 Nov '21

External Email - Use Caution Dr. Jeffrey Spielberg is accepting applications for a *Postdoctoral Researcher position* in the *Connectomics of Anxiety and Depression* Lab at the University of Delaware. The researcher will contribute to an ongoing NIMH-funded R01 grant examining longitudinal change in brain networks that contribute to anxiety development during early adolescence, with a focus on pubertal hormones. The ideal candidate will have a strong background in programming and MRI analysis, along with an interest in adolescent development, emotion/motivation, and/or anxiety, although all applications are encouraged. Clinical training or experience with network analysis methods are not required, but would be considered an asset. Applications from any area of Psychology/Neuroscience are encouraged, although previous experience with human MRI is necessary. The primary duties of the postdoctoral researcher will be to analyze MRI data and write manuscripts for publication. In addition, the researcher will have the opportunity to learn and apply cutting-edge network-analysis methods (e.g., graph theory) to understand the network basis for anxiety. The position would last for a two-year period with potential for renewal. If you are interested in being considered for the position, please send a current CV, a brief statement of interest that outlines your qualifications for the position, reprints of selected papers, and the names of three professional references to Dr. Jeffrey Spielberg at jmsp(a)udel.edu. For more information on the lab’s work, see http://secure-web.cisco.com/10kRxO4QDT9UHmYJygXW-LnOe5rPLvNlHrCty61ZS9vJPOg… *QUALIFICATIONS:* - Ph.D. in psychology, neuroscience, or related disciplines - Experience processing and analyzing structural, functional, and/or diffusion MRI data - Proficiency in programming (e.g., MATLAB, python) - Previous human MRI publications - Interest in adolescent development, emotion/motivation, and/or anxiety - Clinical training (e.g., SCID/KSADS administration) and/or experience with network analysis (e.g., graph theory) are not required, but would be considered an asset -- Jeffrey M. Spielberg, Ph.D. Assistant Professor, Clinical Science Department of Psychological and Brain Sciences University of Delaware Newark, DE 19716 Office: 307 McKinly Laboratory Lab: Suite 405 Wolf Hall Phone: 302.831.7078 Email: jmsp(a)udel.edu Website: http://secure-web.cisco.com/12t4roXdLMzWMowFXG4PN_M7hKCruxhrARdichNITr9XaE3…

1 0

Basic question
by Rosalia Dacosta Aguayo 22 Nov '21

22 Nov '21

External Email - Use Caution Dear Freesurfer team, I know this is a basic question, but I would like to be sure before proceeding. Are those statements below right? For cortical thickness, I should covariate for age and sex For volume, I should covariate only for TBV Thank you for your time and your patience. Best wishes, Rosie

3 4

Full-time postbac position
by Jeffrey Spielberg 22 Nov '21

22 Nov '21

External Email - Use Caution The Connectomics of Anxiety and Depression (CAD) Lab at the University of Delaware is hiring a full time postbac research assistant. The individual will contribute to an ongoing NIMH-funded R01 grant examining longitudinal change in brain networks that contribute to anxiety development during early adolescence, with a focus on pubertal hormones. For more information about lab research, see https://secure-web.cisco.com/1XTw1e_gdvZyZtu3koOqRfU0YpRu5oW2IcicmH5PlL7GLy… The position is temporary and may be renewed on a 12-month basis, dependent upon available funding and performance. The position is ideal for motivated individuals interested in applying to graduate school in psychology or neuroscience in the future, as it will offer the opportunity for mentored research projects and developing manuscripts for publication. Ultimately, a 2-year commitment is strongly preferred. Responsibilities include running participants through clinical assessments and MRI sessions, processing and scoring data, monitoring the quality of data, and organizing data collection efforts, among other research-related activities. To apply for this position, please see https://secure-web.cisco.com/174KT1-gsLISDr2_JbAVOow6GCBisgr6KbQ-eXlLPvuAgc… -- Jeffrey M. Spielberg, Ph.D. Assistant Professor, Clinical Science Department of Psychological and Brain Sciences University of Delaware Newark, DE 19716 Office: 307 McKinly Laboratory Lab: Suite 405 Wolf Hall Phone: 302.831.7078 Email: jmsp(a)udel.edu Website: http://secure-web.cisco.com/1XSZf3m682pkdBmuzqZv3aSTWP0hBnwES55E5wx_Cbe__is…

1 0

Re: [Freesurfer] Pipeline errors - matlab
by fsbuild 22 Nov '21

22 Nov '21

External Email - Use Caution The Matlab MCRv84 release used by Freesurfer is too old to be supported on MacOS 11 Big Sur by The Mathworks (looks like you are running MacOS 11.5 beta 2 release). There are also error reports similar to yours with old versions of Matlab on different versions of MacOS.  From what I read on The Mathworks web site, it looks like a fix was made in R2017b, but I don’t if that release will work with freesurfer or MacOS 11. If you want to try that release, you could do the following. Download R2017b from,https://secure-web.cisco.com/1cphCEkfouFma1YYMWmPUTPpDCt3HnegC93vKeXgp… After downloading, double click on the zip archive to get the dmg archive.  Then double click on the dmg archive to see the installer pkg. When you double click on the installer pkg to run it and go thru the steps you will get to a window showing the install path.  Type in the path /Applications/freesurfer in the installer window and then click on Next. Then when the installer finishes you should have a subdirectory /Applications/freesurfer/v93 The new v93 subdirectory needs to look like it has the MCRv84 distribution name.  So save the MCRv84 distribution by just moving it aside as something with a different name like WAS_MCRv84 $ sudo cd /Applications/freesurfer $ sudo mv  MCRv84  WAS_MCRv84 Use a soft link to allow the new v93 directory to be accessed with the old MCRv84 directory name ... $ sudo ln  -s  v93 MCRv84 Now when you ls /Applications/freesurfer/MCRv84 you will really see the newer R2017b matlab release under the v93 subdirectory. The Matlab installer will probably say to set the environment variable DYLD_LIBRARY_PATH and show paths with /Applications/freesurfer/v93   I think that is OK since now there is both the real subdirectory /Applications/freesurfer/v93 and also the soft link MCRv84 that points to it. If you want to put everything back to the way it was then, $ sudo cd /Applications/freesurfer/7.2.0 $ sudo rm MCRv84 $ sudo mv  WAS_MCRv84  MCRv84 - R. On Nov 22, 2021, at 00:15, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience <ladn(a)email.gwu.edu> wrote:        External Email - Use Caution        Hello Eugenio, Thank you so much for your response. Here is a large section of the error message I got while running hippocampal subfields. Please let me know if more details are needed! ------------------------------------------------------------------------       Segmentation violation detected at Fri Nov 12 14:26:43 2021------------------------------------------------------------------------Configuration:  Crash Decoding     : Disabled  Current Visual     : Quartz  Default Encoding   : ISO-8859-1  MATLAB Architecture: maci64  MATLAB Root        : /Applications/freesurfer/MCRv84  MATLAB Version     : 8.4.0.150421 (R2014b)  Operating System   : Darwin 20.6.0 Darwin Kernel Version 20.6.0: Mon Aug 30 06:12:21 PDT 2021; root:xnu-7195.141.6~3/RELEASE_X86_64 x86_64  Processor ID       : x86 Family 6 Model 85 Stepping 4, 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      : QuartzFault Count: 1Abnormal termination:Segmentation violationRegister State (from fault):  RAX = 0000000000000000  RBX = 0000000000000000  RCX = 0000000000000000  RDX = 0000000000000000  RSP = 0000000000000000  RBP = 0000000000000000  RSI = 0000000000000000  RDI = 0000000000000000   R8 = 0000000000000000   R9 = 0000000000000000  R10 = 0000000000000000  R11 = 0000000000000000  R12 = 000070000c6edd00  R13 = 00007fff203e54bd  R14 = 00007fff87147d38  R15 = 000070000c6edda0  RIP = 0000000000003002  RFL = 00007f9f5ca7bc80   CS = 0000000000000000   FS = 0000000000000000   GS = 000000010a6d1560Stack Trace (from fault):[  0] 0x000000010a320e64 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052[  1] 0x000000010a324a2a /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906[  2] 0x000000010a324477 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119[  3] 0x000000010dcd9b7a /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146[  4] 0x000000010dcd9e58 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880[  5] 0x000000010dcd7733 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275[  6] 0x00007fff20465d7d           /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029[  7] 0x0000000000000000                                   <unknown-module>+00000000[  8] 0x0000000107d7e6ca /Applications/freesurfer/lib/gcc/lib/libstdc++.6.dylib+00063178 _ZNK10__cxxabiv121__vmi_class_type_info11__do_upcastEPKNS_17__class_type_infoEPKvRNS1_15__upcast_resultE+00000186If this problem is reproducible, please submit a Service Request via:    MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1YLRLijXwFNY_9s31qpWP7OijPJA7VNOM42hUT_… technical support engineer might contact you with further information.Thank you for your help.** This crash report has been saved to disk as /Users/ajobsaid/matlab_crash_dump.7498-1 **Caught "std::exception" Exception message is:FatalException------------------------------------------------------------------------          std::terminate() detected at Fri Nov 12 14:26:43 2021------------------------------------------------------------------------Configuration:  Crash Decoding     : Disabled  Current Visual     : Quartz  Default Encoding   : ISO-8859-1  MATLAB Architecture: maci64  MATLAB Root        : /Applications/freesurfer/MCRv84  MATLAB Version     : 8.4.0.150421 (R2014b)  Operating System   : Darwin 20.6.0 Darwin Kernel Version 20.6.0: Mon Aug 30 06:12:21 PDT 2021; root:xnu-7195.141.6~3/RELEASE_X86_64 x86_64  Processor ID       : x86 Family 6 Model 85 Stepping 4, 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      : QuartzFault Count: 2Abnormal termination:Segmentation violationRegister State (from fault):  RAX = 0000000000000000  RBX = 0000000000000000  RCX = 0000000000000000  RDX = 0000000000000000  RSP = 0000000000000000  RBP = 0000000000000000  RSI = 0000000000000000  RDI = 0000000000000000   R8 = 0000000000000000   R9 = 0000000000000000  R10 = 0000000000000000  R11 = 0000000000000000  R12 = 000070000c6edd00  R13 = 00007fff203e54bd  R14 = 00007fff87147d38  R15 = 000070000c6edda0  RIP = 0000000000003002  RFL = 00007f9f5ca7bc80   CS = 0000000000000000   FS = 0000000000000000   GS = 000000010a6d1560Stack Trace (from fault):[  0] 0x000000010a320e64 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052[  1] 0x000000010a324a2a /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906[  2] 0x000000010a324477 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119[  3] 0x000000010dcd9b7a /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146[  4] 0x000000010dcd9e58 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880[  5] 0x000000010dcd7733 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275[  6] 0x00007fff20465d7d           /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029[  7] 0x0000000000000000                                   <unknown-module>+00000000[  8] 0x0000000107d7e6ca /Applications/freesurfer/lib/gcc/lib/libstdc++.6.dylib+00063178 _ZNK10__cxxabiv121__vmi_class_type_info11__do_upcastEPKNS_17__class_type_infoEPKvRNS1_15__upcast_resultE+00000186Abnormal termination:std::terminate()Register State (captured):  RAX = 0000000000000000  RBX = 000070000c6f3578  RCX = 0000000000000000  RDX = 0000000000000000  RSP = 000070000c6f2e10  RBP = 000070000c6f3130  RSI = 0000000000000000  RDI = 0000000000000000   R8 = 0000000000000000   R9 = 0000000000000000  R10 = 0000000000000000  R11 = 0000000000000000  R12 = 000070000c6f3d00  R13 = 0000000000000000  R14 = 00007fff80719d70  R15 = 0000000000000000  RIP = 000000010a325e8b  RFL = 0000000000000000   CS = 0000000100000001   FS = fffffffffffffff8   GS = 0000000000000000Stack Trace (captured):[  0] 0x000000010a320e64 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052[  1] 0x000000010a324a2a /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906[  2] 0x000000010a324477 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119[  3] 0x000000010dcd9b7a /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146[  4] 0x000000010dcd9e58 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880[  5] 0x000000010dcd93a0 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00385952 _Z32mnRunPathDependentInitializationv+00001136[  6] 0x000000010dcd8e54 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00384596 _Z22mnInstallCrashHandlersv+00000420[  7] 0x0000000107d7c698 /Applications/freesurfer/lib/gcc/lib/libstdc++.6.dylib+00054936 _ZN10__cxxabiv111__terminateEPFvvE+00000008[  8] 0x000000010de4b7f1 /Applications/freesurfer/MCRv84/bin/maci64/libmwiqm.dylib+00075761 _ZN3iqm3Iqm15setupIqmFcnPtrsEv+00004945[  9] 0x0000000108119005 /Applications/freesurfer/MCRv84/bin/maci64/libmwservices.dylib+00196613 _ZN10eventqueue18UserEventQueueImpl5flushEv+00001205[ 10] 0x000000011b343a65 /Applications/freesurfer/MCRv84/bin/maci64/libmwuix.dylib+00043621 _Z25isHandleUserEventCallbackPFvPvE+00000501[ 11] 0x00000001081e8a45 /Applications/freesurfer/MCRv84/bin/maci64/libmwservices.dylib+01047109 _Z21svWS_ProcessCallbacksv+00016693[ 12] 0x00000001081e4152 /Applications/freesurfer/MCRv84/bin/maci64/libmwservices.dylib+01028434 _Z25svWS_ProcessPendingEventsiib+00000834[ 13] 0x00000001081e3e5e /Applications/freesurfer/MCRv84/bin/maci64/libmwservices.dylib+01027678 _Z25svWS_ProcessPendingEventsiib+00000078[ 14] 0x000000010dc9818f /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095[ 15] 0x000000010dc9849f /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335[ 16] 0x000000010dc7ed1b /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059[ 17] 0x00007fff204208fc            /usr/lib/system/libsystem_pthread.dylib+00026876 _pthread_start+00000224[ 18] 0x00007fff2041c443            /usr/lib/system/libsystem_pthread.dylib+00009283 thread_start+00000015If this problem is reproducible, please submit a Service Request via:    MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1YLRLijXwFNY_9s31qpWP7OijPJA7VNOM42hUT_… technical support engineer might contact you with further information.Thank you for your help.** This crash report has been saved to disk as /Users/ajobsaid/matlab_crash_dump.7498-2 **MATLAB is exiting because of fatal error/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 37:  7498 Killed: 9               "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $argsDarwin CCAPSY-0GYM0XV 20.6.0 Darwin Kernel Version 20.6.0: Mon Aug 30 06:12:21 PDT 2021; root:xnu-7195.141.6~3/RELEASE_X86_64 x86_64T1 hippocampal subfields exited with ERRORS at Fri Nov 12 14:26:43 EST 2021Thanks! AlexOn Tue, Nov 16, 2021 at 12:05 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote:Dear Alex,Can you please send us the full output?Cheers,/EugenioJuan Eugenio IglesiasSenior research fellowCMIC (UCL), MGH (HMS) and CSAIL (MIT)MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/15Cdhj3LNq_RwvAkNk-hat1i8c0CX7qVDA2sbNI… 12 Nov 2021, at 23:39, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience <ladn(a)email.gwu.edu> wrote:        External Email - Use Caution        Hello Freesurfer experts! Hope that you are all well. I am having errors when running hippocampal subfields and thalamic subfields. When in the error log for the hippocampal pipeline, this is part of the error that I got: MATLAB is exiting because of fatal error/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 37:  7498 Killed: 9               "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $argsDarwin CCAPSY-0GYM0XV 20.6.0 Darwin Kernel Version 20.6.0: Mon Aug 30 06:12:21 PDT 2021; root:xnu-7195.141.6~3/RELEASE_X86_64 x86_64T1 hippocampal subfields exited with ERRORS at Fri Nov 12 14:26:43 EST 2021Please let me know if additional info is needed. Thank you so much, Alex_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1qlSMaH5lwydIo7lfolBJmu5uEEfo93ZBD9Ai7… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1qnXBMbD40ZVLX3RwULANcZQDif3uUyu5MINeI… information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1KdkqTsFrq4x5-8J0JkQZkrfQUJL1hlCw5kHzDn… If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer