Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

make_average_subject error
by Jordan Mullins 14 Apr '21

14 Apr '21

External Email - Use Caution Hello, I am trying to create an average subject from a set of subjects, but keep getting an error that says "mghRead(mri/norm.mgz, -1): could not open file". I've read that several others have solved this issue by installing the patch available at http://secure-web.cisco.com/1holHARxUGo27ZLvlj5vX0sbezsRgmRaNdE1T-Z728EASqG…. I did this, but continue to get the same error. I'm working with Freesurver Version 6.0.0 and MacOS Big Sur Version 11.2.3. I've attached the recon-all.log below, but please let me know if you need additional information. Any insight on this would be appreciated! Thank you! Jordan -- *Jordan L. Mullins, B.A.* Doctoral Student, Department of Psychology University of California, Riverside http://secure-web.cisco.com/1mshZJHsrG2WjtWWNRNV7vunyA6LicMMo4DqXl-CgSaJWwH…

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recon-all transformations: raw nii to T1.mgz
by Peled, Noam 14 Apr '21

14 Apr '21

Hello, I was running recon-all on a raw T1 image with the following properties: dimensions: 126 x 144 x 88 voxel sizes: 1.777778, 1.777778, 1.780000 Orientation: PSL Besides the raw T1, I have other nii files with the same dimensions and orientation that I want to visualize on top of the recon-all output T1.mgz. How can I run the same transformations (and reslicing) that were used in recon-all (from my raw nii file to T1.mgz) on the other nii files? Thanks! Noam

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mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter
by Camerino, I.L. (Ileana) 14 Apr '21

14 Apr '21

External Email - Use Caution Dear Freesurfer experts, I am running recon all as part of the tractography pipeline on a group of stroke patients. This is are the first lines of my log file: /opt/freesurfer/6.0/bin/recon-all -s sub-056 -i /project/3015068.01/ilecam/Reolang/Data/sub-056/MP2RAGE_denoised_roi.nii.gz -all -sd /project/3015068.01/ilecam/Reolang/Freesurfer/ -qcache subjid sub-056 setenv SUBJECTS_DIR /project/3015068.01/ilecam/Reolang/Freesurfer FREESURFER_HOME /opt/freesurfer/6.0 Actual FREESURFER_HOME /opt/freesurfer/6.0 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Recon all did not finished successfully because a watershed error: Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. I added many wm control-points to nu.mgz and to T1.mgz but when I re-run recon-all I still get the same error. Please can you help me to solve this problem? Thank you in advance Best regards, Ileana Camerino PhD candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognition Spinozabuilding Room B02.25 Montessorilaan 3, 6525 HR Nijmegen The Netherlands Tel. +31-24 3612618

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MGH/Harvard: Postdoc position in 7T brainstem fMRI and non-invasive vagus nerve stimulation
by Jacobs, H (NP) 14 Apr '21

14 Apr '21

External Email - Use Caution Postdoc Position in the Department of Radiology, Massachusetts General Hospital / Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in Boston, Massachusetts, has an opening for highly qualified individuals at the post-doctoral level to work with Dr. Heidi Jacobs. The Jacobs lab is part of the Gordon Center for Medical Imaging at MGH and focused on improving the early detection and early treatment of Alzheimer’s disease. The lab focuses on the neuromodulatory subcortical nuclei, in particular the locus coeruleus, using a variety of approaches, including 7T MRI, PET imaging, pupil measurements, physiological recording, blood-based markers and cognitive assessments. This postdoc will be involved in a new NIA-funded R01 project using 7T imaging and non-invasive stimulation of the vagus nerve to modulate cognitive performance and locus coeruleus activity in older individuals at risk for Alzheimer’s disease. Our team and this project are closely affiliated with the Harvard Aging Brain Study (HABS). The position is available from June 2021. Most of the work in this project will be performed at the Athinoula A. Martinos Center for Biomedical Imaging, Charlestown Navy Yard. The candidate will be part of ongoing collaborations and be able to work in a stimulating and inspiring environment. The Department of Radiology at MGH is equipped with the first mobile PET/CT, the first brain PET/MRI, the first whole-body PET/MRI in the USA and several MRI scanners, including two 7T ultra-high-field scanner. It is equipped with a large-scale shared memory computing facility for parametric image analysis, tomographic reconstruction, Monte Carlo simulation, and other computationally intensive research applications. Our research group values open communication, motivation, optimism, mutual respect, teamwork, and innovative thinking. Dr. Jacobs is highly committed to individualized mentoring to help trainees achieve the most out of their postdoctoral candidature and to move forward in their career. At a minimum, the training environment will include professional development, one-on-one meetings, group lab meetings, frequent seminars and journal clubs, opportunities to present their work at national and international scientific conferences (i.e. Human Amyloid Imaging, Alzheimer’s Association International Conference, OHBM), and manuscript preparation for publication in high impact journals. In addition, Dr. Jacobs has a strong funding record and will strongly encourage and provide mentorship in grant applications. Requirements: Candidates should have a Ph.D. in Cognitive Neuroscience, Computational Neuroscience, Medical Physics, Computer Science, Biomedical Engineering or related disciplines. Strong analytical, quantitative and programming skills are essential (e.g., fMRI-physiological data analyses, data modeling, simulations). Prior experience in fMRI, non-invasive neurostimulation methods and physiological investigation is advantageous. The candidate should be highly motivated, a strong communicator, possess internal drive to learn independently, but also be comfortable with working as part of a larger collaborative team. A real necessity is a passion for science, strong scientific writing and organizational skills, and a positive attitude. Experience in Alzheimer’s disease dementia or aging would be beneficial. MGH & HMS are equal-opportunity, affirmative action employers. Women and minority candidates are encouraged to apply. [cid:image001.png@01D730FB.C114F660]Apply: The successful candidate will have joint appointments at MGH and HMS. If interested, please send your CV, letter describing interests, background, major achievements, skills, goals and contact information for three professional references. Please send application materials to Dr. Heidi Jacobs, Assistant Professor of Radiology, at hjacobs(a)mgh.harvard.edu<mailto:hjacobs@mgh.harvard.edu>

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MGH/Harvard: Brainstem PET and DTI postdoc position
by Jacobs, H (NP) 14 Apr '21

14 Apr '21

External Email - Use Caution Postdoc Position in the Department of Radiology, Massachusetts General Hospital / Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in Boston, Massachusetts, has an opening for highly qualified individuals at the post-doctoral level to work with Dr. Heidi Jacobs. The Jacobs lab is part of the Gordon Center for Medical Imaging at MGH and focused on improving the early detection and early treatment of Alzheimer’s disease. The lab focuses on the neuromodulatory subcortical nuclei, in particular the locus coeruleus, using a variety of approaches, including 7T MRI, PET imaging, pupil measurements, physiological recording, blood-based markers and cognitive assessments. This postdoc will be involved in a new NIA-funded project working on new methods in PET and diffusion imaging to examine tau propagation in aging and Alzheimer’s disease. Our team and this project is embedded within the Harvard Aging Brain Study (HABS). Ideal start date is around July/August 2021. Most of the work in this project will be performed at the Athinoula A. Martinos Center for Biomedical Imaging, Charlestown Navy Yard. The candidate will be part of ongoing collaborations and be able to work in a stimulating and inspiring environment. The Department of Radiology at MGH is equipped with the first mobile PET/CT, the first brain PET/MRI, the first whole-body PET/MRI in the USA and several MRI scanners, including two 7T ultra-high-field scanner. It is equipped with a large-scale shared memory computing facility for parametric image analysis, tomographic reconstruction, Monte Carlo simulation, and other computationally intensive research applications. Our research group values open communication, motivation, optimism, mutual respect, teamwork, and innovative thinking. Dr. Jacobs is highly committed to individualized mentoring to help trainees achieve the most out of their postdoctoral candidature and to move forward in their career. At a minimum, the training environment will include professional development, one-on-one meetings, group lab meetings, frequent seminars and journal clubs, opportunities to present their work at national and international scientific conferences (i.e. Human Amyloid Imaging, Alzheimer’s Association International Conference, OHBM), and manuscript preparation for publication in high impact journals. In addition, Dr. Jacobs has a strong funding record and will strongly encourage and provide mentorship in grant applications. Requirements: Candidates should have a Ph.D. in Cognitive Neuroscience, Computational Neuroscience, Medical Physics, Computer Science, Biomedical Engineering or related disciplines. Strong analytical, quantitative and programming skills as well as expertise in diffusion imaging are essential. Prior experience in PET is advantageous. The candidate should be highly motivated, a strong communicator, possess internal drive to learn independently, but also be comfortable with working as part of a larger collaborative team. A real necessity is a passion for science, strong scientific writing and organizational skills, and a positive attitude. Experience in Alzheimer’s disease dementia or aging would be beneficial. MGH & HMS are equal-opportunity, affirmative action employers. Women and minority candidates are encouraged to apply. [cid:image001.png@01D730FB.32A4E1B0]Apply: The successful candidate will have joint appointments at MGH and HMS. If interested, please send your CV, letter describing interests, background, major achievements, skills, goals and contact information for three professional references. Please send application materials to Dr. Heidi Jacobs, Assistant Professor of Radiology, at hjacobs(a)mgh.harvard.edu<mailto:hjacobs@mgh.harvard.edu>

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preproc-sess
by Manenti, Giorgio 13 Apr '21

13 Apr '21

External Email - Use Caution Dear Experts, I’m encountering a problem when running the preproc-sess on my functional data. When using the flag -surface subject hemi i am getting ":ERROR: source volume is neither source nor target of the registration”. There is any alternative way to get the surfaces? Many thanks for your help Best Giorgio

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Postdoc Position at the Buffalo Neuroimaging Analysis Center
by Michael Dwyer 13 Apr '21

13 Apr '21

External Email - Use Caution Dear all, The Buffalo Neuroimaging Analysis Center (BNAC), an interdisciplinary organization that is part of the Department of Neurology of The State University of New York at Buffalo (http://secure-web.cisco.com/15d0nEH6vnvRtzz4rIsQT20HCiBgIHP2i3Sb709ItZJSzog…) is looking for a post-doctoral fellow to be part of upcoming studies combining novel PET tracers with other imaging modalities to understand the pathology and progression of multiple sclerosis and other neurological diseases and disorders. Ideal start date is June 2021. The research program will be conducted at the University at Buffalo, Buffalo, NY, under the supervision of Professor Robert Zivadinov and Associate Professors Michael Dwyer and Ferdinand Schweser. The candidate will be part of ongoing and new collaborations and be able to work in a stimulating and inspiring environment. The fellow is expected to work closely with the team to plan and apply state-of-the-art PET approaches and fusion with MRI and other modalities. In addition, he/she will have the opportunity to develop new skills, analyze datasets, apply for grants, and develop a strong network of collaborations. The BNAC team includes neurologists, computer scientists, MR physicists, and many others working to uncover new ways to use neuroimaging to extend the boundaries of our current knowledge about neurological diseases and disorders like multiple sclerosis, Alzheimer’s disease, Parkinson’s disease and stroke among others. The BNAC is equipped with multiple 3T MRIs with active research agreements, a 9.4T Bruker MRI with CryoProbe and a prototype microPET insert, and a dedicated PET/CT research scanner. Requirements: • Ph.D. in neuroimaging, computer science, biomedical engineering, neuropsychology, physics, statistics, or a related field • Experience in statistical techniques, programming, and scripting • Substantial experience with PET imaging acquisition and analysis • Good record of scientific publications Additional preferred qualifications: • Experience with structural MRI, DTI, and/or fMRI • Clinical or research experience with aging and/or neurodegenerative disorders • Pre-clinical experience with MRI, CT, and/or PET image analysis To apply please contact Devon Oship at doship(a)bnac.net. -- Michael G. Dwyer, Ph.D. Associate Professor of Neurology and Biomedical Informatics Director, Neuroinfomatics Development and IT Units Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdwyer(a)bnac.net (716) 859-7065

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Re: [Freesurfer] Freeview will not run
by fsbuild 13 Apr '21

13 Apr '21

External Email - Use Caution Hello Aaron, The crash report lists issues with running the Qt package and that you are running zsh.   You could try running freeview under “bash” in the terminal window (which was the default in older versions of MacOS - it may tell you how to set that as your default shell). In a new terminal window you could try running, $ bash Check that the X windows distribution for MacOS is installed with,$ which Xquartz/opt/X11/bin/Xquartz If you don’t see that, then install Xquartz from https://secure-web.cisco.com/17-xR4PJeGXKy7MXV6eO9Mq8lIqfRBMTziNE… then try the “which” command again to find Xquartz. Then setup the freesurfer environment, $ export FREESURFER_HOME=/Applications/freesurfer/7.1.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.1.1 FSFAST_HOME       /Applications/freesurfer/7.1.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.1.1/subjects MNI_DIR           /Applications/freesurfer/7.1.1/mni $ which freeview /Applications/freesurfer/7.1.1/bin/freeview$ freeview …. empty freeview window should come up …. You can also run it form the terminal in the same double clicking on the icon in the Finder would do - which should also work, $ open -a /Applications/freesurfer/7.1.1/Freeview.app If you did not use the pkg installer to install freesurfer 7.1.1 (which needs admin privileges), then you could try the installer from, https://secure-web.cisco.com/1zOWcX0vk_HcCYLk0GOYUnNnAjoxNPWBoiPfrB5b6-q-5Y… - R. On Apr 13, 2021, at 01:08, Aaron Switzer <arswitze(a)ucalgary.ca> wrote:        External Email - Use Caution                External Email - Use Caution        Dear FreeSurfer experts,I am having troubles running Freeview on Mac OSX 10.15.7. I have Freesurfer 7.1.1. When I enter ‘freeview’ into terminal or double click the Freeview.app in FREESURFER_HOME, it crashes and I get the following error: aaronswitzer@Aarons-MacBook-Pro-2 ~ % freeview/Applications/freesurfer/7.1.1/bin/freeview: line 2:  2037 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“ (full error report below)I’ve gone through the suggestions given in the mail archive for a similar problem posted on June 14, 2020, to no avail. I have the most up to date X11 (v2.8.1),  FREESURFER_HOME is properly configured, I’ve tried uninstalling and reinstalling freesurfer, I’ve tried deleting edu.harvard.mgh.nmr.plist, and I tried building the freeview.zip file from GitHub.. Is there anything else I can try?Thank you for your help,Aaron

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Freeview will not run
by Aaron Switzer 13 Apr '21

13 Apr '21

External Email - Use Caution Dear FreeSurfer experts, I am having troubles running Freeview on Mac OSX 10.15.7. I have Freesurfer 7.1.1. When I enter ‘freeview’ into terminal or double click the Freeview.app in FREESURFER_HOME, it crashes and I get the following error: aaronswitzer@Aarons-MacBook-Pro-2 ~ % freeview /Applications/freesurfer/7.1.1/bin/freeview: line 2: 2037 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“ (full error report below) I’ve gone through the suggestions given in the mail archive for a similar problem posted on June 14, 2020, to no avail. I have the most up to date X11 (v2.8.1), FREESURFER_HOME is properly configured, I’ve tried uninstalling and reinstalling freesurfer, I’ve tried deleting edu.harvard.mgh.nmr.plist, and I tried building the freeview.zip file from GitHub. Is there anything else I can try? Thank you for your help, Aaron Process: freeview [2117] Path: /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview Identifier: com.freesurfer.freeview Version: 0 Code Type: X86-64 (Native) Parent Process: zsh [2089] Responsible: Terminal [385] User ID: 501 Date/Time: 2021-04-12 22:56:19.290 -0600 OS Version: Mac OS X 10.15.7 (19H524) Report Version: 12 Bridge OS Version: 3.0 (14Y908) Anonymous UUID: C4040AA1-B39A-9CDF-C9B1-A6690AB8C713 Time Awake Since Boot: 1800 seconds System Integrity Protection: enabled Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000029 Exception Note: EXC_CORPSE_NOTIFY Termination Signal: Segmentation fault: 11 Termination Reason: Namespace SIGNAL, Code 0xb Terminating Process: exc handler [2117] VM Regions Near 0x29: --> __TEXT 0000000106f2a000-0000000108552000 [ 22.2M] r-x/rwx SM=COW /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview Application Specific Information: dyld: in dlsym() Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 com.freesurfer.freeview 0x00000001070fb114 0x106f2a000 + 1904916 1 org.qt-project.QtWidgets 0x0000000117a056ed QWidget::event(QEvent*) + 1117 2 org.qt-project.QtWidgets 0x0000000117b16c45 QMainWindow::event(QEvent*) + 277 3 org.qt-project.QtWidgets 0x00000001179c970d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 4 org.qt-project.QtWidgets 0x00000001179cab12 QApplication::notify(QObject*, QEvent*) + 594 5 org.qt-project.QtCore 0x000000011869d564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 6 org.qt-project.QtWidgets 0x0000000117a23a74 0x1179b9000 + 436852 7 org.qt-project.QtWidgets 0x00000001179c970d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 8 org.qt-project.QtWidgets 0x00000001179cab12 QApplication::notify(QObject*, QEvent*) + 594 9 org.qt-project.QtCore 0x000000011869d564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 10 org.qt-project.QtGui 0x0000000117f94a74 QGuiApplicationPrivate::processGeometryChangeEvent(QWindowSystemInterfacePrivate::GeometryChangeEvent*) + 516 11 org.qt-project.QtGui 0x0000000117f95420 QGuiApplicationPrivate::processWindowScreenChangedEvent(QWindowSystemInterfacePrivate::WindowScreenChangedEvent*) + 736 12 org.qt-project.QtGui 0x0000000117f73c33 bool QWindowSystemInterfacePrivate::handleWindowSystemEvent<QWindowSystemInterface::SynchronousDelivery>(QWindowSystemInterfacePrivate::WindowSystemEvent*) + 115 13 libqcocoa.dylib 0x000000011b76ac77 0x11b74c000 + 126071 14 libqcocoa.dylib 0x000000011b764862 0x11b74c000 + 100450 15 libqcocoa.dylib 0x000000011b7642eb 0x11b74c000 + 99051 16 org.qt-project.QtGui 0x0000000117f9e1dc QWindowPrivate::create(bool, unsigned long long) + 140 17 org.qt-project.QtWidgets 0x00000001179f2e31 QWidgetPrivate::create() + 1201 18 org.qt-project.QtWidgets 0x00000001179f1b22 QWidget::create(unsigned long long, bool, bool) + 322 19 org.qt-project.QtWidgets 0x0000000117b174d7 QMainWindow::setUnifiedTitleAndToolBarOnMac(bool) + 55 20 com.freesurfer.freeview 0x00000001070e9857 0x106f2a000 + 1833047 21 com.freesurfer.freeview 0x00000001070e38fe 0x106f2a000 + 1808638 22 com.freesurfer.freeview 0x00000001070247ea 0x106f2a000 + 1026026 23 libdyld.dylib 0x00007fff6b7b3cc9 start + 1 Thread 1: 0 libsystem_pthread.dylib 0x00007fff6b9b3b68 start_wqthread + 0 Thread 2:: Dispatch queue: com.apple.dock.fullscreen 0 dyld 0x0000000120e0089a ImageLoader::trieWalk(unsigned char const*, unsigned char const*, char const*) + 194 1 dyld 0x0000000120e0a400 ImageLoaderMachOCompressed::findShallowExportedSymbol(char const*, ImageLoader const**) const + 112 2 dyld 0x0000000120e04075 ImageLoaderMachO::findExportedSymbol(char const*, bool, char const*, ImageLoader const**) const + 37 3 dyld 0x0000000120dfcb1a ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 254 4 dyld 0x0000000120dfcbbe ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 5 dyld 0x0000000120dfcbbe ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 6 dyld 0x0000000120dfcbbe ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 7 dyld 0x0000000120dfcbbe ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 8 dyld 0x0000000120dfcbbe ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 9 dyld 0x0000000120dfccda ImageLoader::findExportedSymbolInImageOrDependentImages(char const*, ImageLoader::LinkContext const&, ImageLoader const**) const + 88 10 dyld 0x0000000120dfa3c3 dlsym_internal + 401 11 libdyld.dylib 0x00007fff6b79fa09 dlsym + 195 12 com.apple.SkyLight 0x00007fff60b70124 __loginframework_vtable_block_invoke + 564 13 libdispatch.dylib 0x00007fff6b75a658 _dispatch_client_callout + 8 14 libdispatch.dylib 0x00007fff6b75b7de _dispatch_once_callout + 20 15 com.apple.SkyLight 0x00007fff60b71a85 SLSCopyCurrentSessionPropertiesInternalBridge + 366 16 com.apple.SkyLight 0x00007fff60a56ee3 SLSessionCopyCurrentDictionary + 12 17 com.apple.AppKit 0x00007fff2ea9670a -[NSDockConnection _makeConnectionIfNeededWithRetryInterval:onDemand:] + 47 18 com.apple.AppKit 0x00007fff2ea966cf __35-[NSDockConnection startConnection]_block_invoke.41 + 45 19 libdispatch.dylib 0x00007fff6b7596c4 _dispatch_call_block_and_release + 12 20 libdispatch.dylib 0x00007fff6b75a658 _dispatch_client_callout + 8 21 libdispatch.dylib 0x00007fff6b75fc44 _dispatch_lane_serial_drain + 597 22 libdispatch.dylib 0x00007fff6b7605d6 _dispatch_lane_invoke + 363 23 libdispatch.dylib 0x00007fff6b769c09 _dispatch_workloop_worker_thread + 596 24 libsystem_pthread.dylib 0x00007fff6b9b4a3d _pthread_wqthread + 290 25 libsystem_pthread.dylib 0x00007fff6b9b3b77 start_wqthread + 15 Thread 3: 0 libsystem_pthread.dylib 0x00007fff6b9b3b68 start_wqthread + 0 Thread 4: 0 libsystem_pthread.dylib 0x00007fff6b9b3b68 start_wqthread + 0 Thread 5: 0 libsystem_pthread.dylib 0x00007fff6b9b3b68 start_wqthread + 0 Thread 6: 0 libsystem_pthread.dylib 0x00007fff6b9b3b68 start_wqthread + 0 Thread 7: 0 libsystem_pthread.dylib 0x00007fff6b9b3b68 start_wqthread + 0 Thread 8: 0 libsystem_pthread.dylib 0x00007fff6b9b3b68 start_wqthread + 0 Thread 9: 0 libsystem_pthread.dylib 0x00007fff6b9b3b68 start_wqthread + 0 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000108562738 rbx: 0x00007ffee8cd3698 rcx: 0x0000000000010000 rdx: 0x0000000117a056dd rdi: 0x0000000000000001 rsi: 0x00007ffee8cd2708 rbp: 0x00007ffee8cd21c0 rsp: 0x00007ffee8cd21b0 r8: 0x0000000000000000 r9: 0x0000000000000100 r10: 0x0000000120e86a98 r11: 0x000000011869d5b0 r12: 0x00007f907677bf30 r13: 0x00007ffee8cd3698 r14: 0x00007ffee8cd2708 r15: 0x00007ffee8cd2708 rip: 0x00000001070fb114 rfl: 0x0000000000010207 cr2: 0x0000000000000029 Logical CPU: 4 Error Code: 0x00000004 (no mapping for user data read) Trap Number: 14 Binary Images: 0x106f2a000 - 0x108551fff +com.freesurfer.freeview (0) <2C3FDDEC-DEC1-3036-B993-7A638DA1BECD> /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview 0x1179b9000 - 0x117df7ff7 +org.qt-project.QtWidgets (5.12 - 5.12.7) <EF671B84-7965-3C74-89DF-09C3FA9096CA> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtWidgets.framework/Versions/5/QtWidgets 0x117f5e000 - 0x1183aafe7 +org.qt-project.QtGui (5.12 - 5.12.7) <9CC34B01-AE4A-3FF2-AC1B-DE08B8FBBBAE> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtGui.framework/Versions/5/QtGui 0x1184b3000 - 0x1189e8ff7 +org.qt-project.QtCore (5.12 - 5.12.7) <AE294CA9-B3EC-3F0E-B67A-509A13C0C913> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtCore.framework/Versions/5/QtCore 0x118b8a000 - 0x118bb3ff7 +org.qt-project.QtPrintSupport (5.12 - 5.12.7) <9AB0608C-8F2E-3FC1-B144-04ECEC6FA634> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtPrintSupport.framework/Versions/5/QtPrintSupport 0x11b74c000 - 0x11b8b2fff +libqcocoa.dylib (0) <14BC2336-68E6-3ACE-B3A9-F21152A64785> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/platforms/libqcocoa.dylib 0x11b8ff000 - 0x11b95dfff +org.qt-project.QtDBus (5.12 - 5.12.7) <3D9A10D9-CB4E-3A1B-8664-BD25993D5FF3> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtDBus.framework/Versions/5/QtDBus 0x11de1a000 - 0x11de3ffff +libqmacstyle.dylib (0) <05CC7ADD-D833-3744-93D6-D859235085A3> 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<793D9643-CD83-3AAC-8B96-88D548FAB620> /usr/lib/libz.1.dylib 0x7fff6b595000 - 0x7fff6b59aff3 libcache.dylib (83) <AF488D13-9E89-35E0-B078-BE37CC5B8586> /usr/lib/system/libcache.dylib 0x7fff6b59b000 - 0x7fff6b5a6fff libcommonCrypto.dylib (60165.120.1) <C7912BE5-993E-3581-B2A0-6AABDC8C5562> /usr/lib/system/libcommonCrypto.dylib 0x7fff6b5a7000 - 0x7fff6b5aefff libcompiler_rt.dylib (101.2) <49B8F644-5705-3F16-BBE0-6FFF9B17C36E> /usr/lib/system/libcompiler_rt.dylib 0x7fff6b5af000 - 0x7fff6b5b8ff7 libcopyfile.dylib (166.40.1) <3C481225-21E7-370A-A30E-0CCFDD64A92C> /usr/lib/system/libcopyfile.dylib 0x7fff6b5b9000 - 0x7fff6b64bfdb libcorecrypto.dylib (866.140.1) <60567BF8-80FA-359A-B2F3-A3BAEFB288FD> /usr/lib/system/libcorecrypto.dylib 0x7fff6b758000 - 0x7fff6b798ff0 libdispatch.dylib (1173.100.2) <CD9C059C-91D9-30E8-8926-5B9CD0D5D4F5> /usr/lib/system/libdispatch.dylib 0x7fff6b799000 - 0x7fff6b7cffff libdyld.dylib (750.6) <789A18C2-8AC7-3C88-813D-CD674376585D> /usr/lib/system/libdyld.dylib 0x7fff6b7d0000 - 0x7fff6b7d0ffb libkeymgr.dylib (30) <DB3337BE-01CA-3425-BD0C-87774FC0CDC0> /usr/lib/system/libkeymgr.dylib 0x7fff6b7d1000 - 0x7fff6b7ddff3 libkxld.dylib (6153.141.16) <32E58B88-2028-3F9D-A833-673ED01BB7AC> /usr/lib/system/libkxld.dylib 0x7fff6b7de000 - 0x7fff6b7deff7 liblaunch.dylib (1738.140.2) <7200E214-9B4D-3B22-9844-4C7892FC890B> /usr/lib/system/liblaunch.dylib 0x7fff6b7df000 - 0x7fff6b7e4ff7 libmacho.dylib (959.0.1) <AA613A9C-961A-3B67-B696-4622FA59FC4E> /usr/lib/system/libmacho.dylib 0x7fff6b7e5000 - 0x7fff6b7e7ff3 libquarantine.dylib (110.40.3) <F234E51D-FD0B-3EE4-B679-AE3EE9C536C3> /usr/lib/system/libquarantine.dylib 0x7fff6b7e8000 - 0x7fff6b7e9ff7 libremovefile.dylib (48) <7C7EFC79-BD24-33EF-B073-06AED234593E> /usr/lib/system/libremovefile.dylib 0x7fff6b7ea000 - 0x7fff6b801ff3 libsystem_asl.dylib (377.60.2) <1563EE02-0657-3B78-99BE-A947C24122EF> /usr/lib/system/libsystem_asl.dylib 0x7fff6b802000 - 0x7fff6b802ff7 libsystem_blocks.dylib (74) <0D53847E-AF5F-3ACF-B51F-A15DEA4DEC58> /usr/lib/system/libsystem_blocks.dylib 0x7fff6b803000 - 0x7fff6b88afff libsystem_c.dylib (1353.100.2) <BBDED5E6-A646-3EED-B33A-91E4331EA063> /usr/lib/system/libsystem_c.dylib 0x7fff6b88b000 - 0x7fff6b88effb libsystem_configuration.dylib (1061.141.1) <0EE84C33-64FD-372B-974A-AF7A136F2068> /usr/lib/system/libsystem_configuration.dylib 0x7fff6b88f000 - 0x7fff6b892fff libsystem_coreservices.dylib (114) <A199156E-058D-3ABB-BCE9-4B9F20DCED0F> /usr/lib/system/libsystem_coreservices.dylib 0x7fff6b893000 - 0x7fff6b89bfff libsystem_darwin.dylib (1353.100.2) <5B12B5DB-3F30-37C1-8ECC-49A66B1F2864> /usr/lib/system/libsystem_darwin.dylib 0x7fff6b89c000 - 0x7fff6b8a3fff libsystem_dnssd.dylib (1096.100.3) <EBB4C2C2-E031-3094-B40A-E67BF261D295> /usr/lib/system/libsystem_dnssd.dylib 0x7fff6b8a4000 - 0x7fff6b8a5ffb libsystem_featureflags.dylib (17) <29FD922A-EC2C-3F25-BCCC-B58D716E60EC> /usr/lib/system/libsystem_featureflags.dylib 0x7fff6b8a6000 - 0x7fff6b8f3ff7 libsystem_info.dylib (538) <8A321605-5480-330B-AF9E-64E65DE61747> /usr/lib/system/libsystem_info.dylib 0x7fff6b8f4000 - 0x7fff6b920ff7 libsystem_kernel.dylib (6153.141.16) <05E98124-C845-374E-A323-8D6CFB60926F> /usr/lib/system/libsystem_kernel.dylib 0x7fff6b921000 - 0x7fff6b968fff libsystem_m.dylib (3178) <00F331F1-0D09-39B3-8736-1FE90E64E903> /usr/lib/system/libsystem_m.dylib 0x7fff6b969000 - 0x7fff6b990fff libsystem_malloc.dylib (283.100.6) <8549294E-4C53-36EB-99F3-584A7393D8D5> /usr/lib/system/libsystem_malloc.dylib 0x7fff6b991000 - 0x7fff6b99effb libsystem_networkextension.dylib (1095.140.2) <F06C65C5-2CBE-313C-96E1-A09240F9FE57> /usr/lib/system/libsystem_networkextension.dylib 0x7fff6b99f000 - 0x7fff6b9a8ff7 libsystem_notify.dylib (241.100.2) <FA22F928-D91B-3AA5-96BB-3186AC0FB264> /usr/lib/system/libsystem_notify.dylib 0x7fff6b9a9000 - 0x7fff6b9b1fef libsystem_platform.dylib (220.100.1) <009A7C1F-313A-318E-B9F2-30F4C06FEA5C> /usr/lib/system/libsystem_platform.dylib 0x7fff6b9b2000 - 0x7fff6b9bcfff libsystem_pthread.dylib (416.100.3) <62CB1A98-0B8F-31E7-A02B-A1139927F61D> /usr/lib/system/libsystem_pthread.dylib 0x7fff6b9bd000 - 0x7fff6b9c1ff3 libsystem_sandbox.dylib (1217.141.2) <051C4018-4345-3034-AC98-6DE42FB8273B> /usr/lib/system/libsystem_sandbox.dylib 0x7fff6b9c2000 - 0x7fff6b9c4fff libsystem_secinit.dylib (62.100.2) <F80872AA-E1FD-3D7E-8729-467656EC6561> /usr/lib/system/libsystem_secinit.dylib 0x7fff6b9c5000 - 0x7fff6b9ccffb libsystem_symptoms.dylib (1238.120.2) <702D0910-5C34-3D43-9631-8BD215DE4FE1> /usr/lib/system/libsystem_symptoms.dylib 0x7fff6b9cd000 - 0x7fff6b9e3ff2 libsystem_trace.dylib (1147.120.1) <BC141783-66D9-3137-A783-211B38E49ADB> /usr/lib/system/libsystem_trace.dylib 0x7fff6b9e5000 - 0x7fff6b9eaff7 libunwind.dylib (35.4) <42B7B509-BAFE-365B-893A-72414C92F5BF> /usr/lib/system/libunwind.dylib 0x7fff6b9eb000 - 0x7fff6ba20ffe libxpc.dylib (1738.140.2) <54EEF402-42C7-3995-BADE-93C48EFC4452> /usr/lib/system/libxpc.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: 2228 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=619.7M resident=0K(0%) swapped_out_or_unallocated=619.7M(100%) Writable regions: Total=359.3M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=359.3M(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 128K 1 Activity Tracing 256K 1 CG backing stores 1600K 4 CoreImage 32K 4 CoreUI image data 188K 2 Dispatch continuations 16.0M 1 Foundation 4K 1 Kernel Alloc Once 8K 1 MALLOC 86.5M 43 MALLOC guard page 32K 7 STACK GUARD 56.0M 10 Stack 12.6M 10 VM_ALLOCATE 68K 8 __DATA 268.5M 306 __DATA_CONST 20K 1 __FONT_DATA 4K 1 __LINKEDIT 393.0M 22 __OBJC_RO 32.3M 1 __OBJC_RW 1908K 2 __TEXT 226.8M 301 __UNICODE 564K 1 mapped file 55.9M 17 shared memory 656K 19 =========== ======= ======= TOTAL 1.1G 764 Model: MacBookPro13,3, BootROM 429.80.1.0.0, 4 processors, Quad-Core Intel Core i7, 2.6 GHz, 16 GB, SMC 2.38f12 Graphics: kHW_IntelHDGraphics530Item, Intel HD Graphics 530, spdisplays_builtin Graphics: kHW_AMDRadeonPro450Item, AMD Radeon Pro 450, spdisplays_pcie_device, 2 GB Memory Module: BANK 0/DIMM0, 8 GB, LPDDR3, 2133 MHz, 0x802C, 0x4D5435324C31473332443450472D30393320 Memory Module: BANK 1/DIMM0, 8 GB, LPDDR3, 2133 MHz, 0x802C, 0x4D5435324C31473332443450472D30393320 AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x15A), Broadcom BCM43xx 1.0 (7.77.111.1 AirPortDriverBrcmNIC-1615.3) Bluetooth: Version 7.0.6f8, 3 services, 27 devices, 1 incoming serial ports Network Service: Wi-Fi, AirPort, en0 Network Service: Thunderbolt Bridge, Ethernet, bridge0 USB Device: USB 3.0 Bus USB Device: Keyboard Hub USB Device: Apple Keyboard USB Device: Mobile Drive USB Device: Apple T1 Controller Thunderbolt Bus: MacBook Pro, Apple Inc., 41.2 Thunderbolt Device: Macintosh, Apple Inc. Thunderbolt Bus: MacBook Pro, Apple Inc., 41.2

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Some func. error during recon-all process
by Horsng Junn 12 Apr '21

12 Apr '21

External Email - Use Caution Hi Yoonho, I'm not an expert but since your inquiry doesn't yet have a reply I thought I'd try to answer it as much as I can. 1. -whitesurf process is preceded over smooth2 and inflated2 in recon-all file, really it is not. why? It seems the second smooth -> inflate -> sphere process is run just to help with the spherical registration and thus the parcellation. I think -whitesurf must be run after that second smooth2 and inflate2 process because it depends on the parcellation result for some anatomical information to make sure the surface geometry is correct, but it still uses the original tessellation result as its basis as the second smoothing might hurt the resulting surface quality. 2. This error first started during -cortribbon process, also occurs in other processes such as -cortparc2, -cortparc3, -hyporelabel, -aparc2aseg, and -wmparc. But these process does not ask for a file called aseg as input if you check it on the homepage. Can you tell me how to fix it? In not just those places but many other places, FS uses some hard-coded input files to read in the segmentation results, transformation matrix, annotation info, etc. I think you just need to provide it with the required segmentation file. Best, Horsng

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