Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Subcortical Segmentation Atlas Question
by Rooks, Tyler 09 Nov '20

09 Nov '20

External Email - Use Caution Good Morning FreeSurfer Developers and Experts, I hope all is well. I am relatively new to the use of FreeSurfer and neuroimaging research in general. I have been looking for any documentation or details regarding the probabilistic atlas used for subcortical segmentation tasks (RB_all_2008-03-26.gca) provided in the ‘average’ directory. Is there any information available or that can be described about what this atlas was generated from or any additional details about the atlas? I am looking for information relating to potential number of subjects used to develop the atlas if that is available or methods used to develop? Additionally, are there any comparisons between this subcortical atlas and other subcortical atlases available? I have found a few comparisons between FreeSurfer and other software/atlases, but nothing comparing the subcortical segmentation directly. Any help or information would be greatly appreciated. Thanks, Tyler Ph.D. Student Medical College of Wisconsin

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Postdoctoral Position in Advanced MRI Acquisition Methods {Disarmed}
by Romy Lorenz 07 Nov '20

07 Nov '20

External Email - Use Caution On behalf of Prof. Nik Weiskopf: Postdoctoral Position in Advanced MRI Acquisition Methods The Dept. of Neurophysics at the Max Planck Institute for Human Cognitive and Brain Sciences (MPI CBS) in Leipzig (Germany) invites applications for a Postdoc Position in Advanced MRI Acquisition Methods. Our vision is to develop and apply microstructure imaging and in-vivo histology using MRI. To resolve the subtle microanatomy and its changes in health and disease, unprecedented spatial resolution, minimal artifact levels and high tissue specificity of the imaging are essential. The postdoc will develop MRI pulse sequences on the latest Siemens 7T Terra and 3T Connectom platforms and integrate them with advanced image reconstruction methods (e.g. BART, Gadgetron). In particular, the successful candidate will work on exciting projects related to one or more of the following: non-Cartesian trajectories, pTx, parallel imaging, balanced steady-state sequences, MR fingerprinting and correction of artifacts using optical motion tracking and field cameras. The ideal candidate must have a strong background in MR physics and pulse sequence programming (ideally IDEA VE), and hold a PhD in physics, biomedical engineering, computer science or a comparable subject. Strong programming skills in C++ are essential and in other high-level languages (e.g. Matlab, Python) and CUDA/OpenCL highly desired. Additional experience in image reconstruction (e.g., ICE, BART) or SPM/FreeSurfer/FSL or similar MRI data processing is highly desired. A proven record of participating in open-source or other larger-scale software projects is highly advantageous. Applicants should demonstrate a consistently outstanding academic record including publications, and be highly proficient in spoken and written English. We offer: • the possibility to conduct truly fundamental research to change the field of neuroimaging, • an international, friendly and highly supportive interdisciplinary environment (working language English), • the chance to work with top researchers (inc. experienced IDEA programmers) from diverse backgrounds in an internationally leading neuroimaging center within the renowned Max Planck Society, • access to world-leading facilities, including a 7T Terra MRI scanner (64-ch Rx, 16-ch Tx), 3T Connectom scanner (300 mT/m gradients) and numerous other 3T scanners, all dedicated to fundamental research with ample scan time, excellent technical support (inc. Siemens collaboration scientist), and the latest peripherals (Skope field camera system, Kineticor PMC). The preferred starting date is immediate but negotiable. The duration of the post is 2 years in the first instance. Remuneration is based on the pay scale of the Max Planck Society. Female and international applicants are particularly encouraged to apply. The Max Planck Society is committed to increasing the number of individuals with disabilities in its workforce and therefore encourages applications from such qualified individuals. To apply, please submit a single PDF file containing a full CV (inc. publication list), personal statement (describing your personal qualifications, research interests and motivation for applying), strong evidence for advanced software development experience (active Github/Gitlab profile or similar), two of your key publications, contact information of three referees and academic certificates (PhD, Diploma/Master, Bachelor certificates). Please submit your application via our online system at http://secure-web.cisco.com/1Quyb0LgQUzWBQ_FxEpT5Iiga4-6frdT13BTaW4I6fJ5Bb-… heading: “PD 10/20”). The closing date for applications is 29th November 2020. Interviews of shortlisted candidates will take place likely via video conference between 7th and 11th December. Further information: For more details about our work go to https://secure-web.cisco.com/1nOyxNbK1yk34qHa1jpkjj3Umj3NsO5YJgpDyqPCNrFWA5…. Leipzig is a vibrant city that has been called “Germany’s new cultural hot spot” by the Guardian and listed as one of the 52 places to go in 2020 by the New York Times. It has a long-standing history of classical music, academic education, and, more recently, modern arts. With its many parks, forests, canals and lakes, Leipzig is a perfect place for recreation, sports, and leisure time. It is located a one hour train ride south of Berlin. If you have any questions, please contact Nik Weiskopf at weiskopf(a)cbs.mpg.de

1 0

Fixing error with pial surface
by Julie Ottoy 06 Nov '20

06 Nov '20

External Email - Use Caution Dear Freesurfer team, I have a question related to fixing the pial surface when a part was missed (see attachment). On the freesurfer website, I only found how to erase the pial when there was too much (see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEditsV6.0 ), but I could not find what to do when there was too little. As there is no white matter in this particular area, it is also not an option to place control points. Also the skull stripping did not change anything: I tried both the freesurfer skull stripping and an in-house skull stripping algorithm. Thank you for your help. Best regards Julie

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repeated measures ANOVA 2x2 two groups two times {Disarmed}
by Agurne Sampedro Calvete 06 Nov '20

06 Nov '20

External Email - Use Caution Dear Freesurfer experts, I am trying to do a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment). Although I have run a paired t-test, now I would like to do a repeated measures anova 2x2, since I am doing the same analyses with other data in other softwares. I am trying to follow the tutorial https://secure-web.cisco.com/1xcEvqAuPN3MsqK1JjC6qoZbooZS3kpB4WEU1Lx8hK28gr…, but I have several doubts when designing the FSGD file as well as the contrasts. How should it be the FSGD file? I have seen in a previous post the following design for the same number fo groups and time points: GroupDescriptorFile 1 Class Subject1 Class Subject2 Variables Tp1vsTp2.GrExp Tp1vsTp2.GrControl Input Subject1_time1 Subject1 1 0 Input Subject1_time2 Subject1 -1 0 Input Subject2_time1 Subject2 0 1 Input Subject2_time2 Subject02 0 -1 Design matrix: 1 0 1 0 1 0 -1 0 0 1 0 1 0 1 0 -1 Contrasts (.mtx files): Tp1vsTp2.GrExp 0 0 1 0 Tp1vsTp2.GrControl 0 0 0 -1 Interaction 0 0 1 -1 Would this design be the correct one to use in this case? Alternatively, could it be this the correct one? GroupDescriptorFile 1 Class Subject1 Class Subject2 Variables Tp1vsTp2 Groupxtime Input Subject1_time1 Subject1 1 1 Input Subject1_time2 Subject1 -1 *-1* Input Subject2_time1 Subject2 1 *-1* Input Subject2_time2 Subject02 -1 1 Design matrix: 1 0 1 1 1 0 -1 -1 0 1 1 -1 0 1 -1 1 Contrasts (.mtx files): Tp1vsTp2 0 0 1 0 Groupxtime Interaction 0 0 0 1 Thank you very much in advance. Kind regards, Agurne Neuropsychology of Severe Medical Conditions Research Team Dpt of Methods and Experimental Psychology Faculty of Psychology and Education University of Deusto neurolab.deusto.es Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3015)

2 4

MRI SNR
by 南修司郎 06 Nov '20

06 Nov '20

External Email - Use Caution Dear expert We are planning multi-center study with the hearing impaired patients using FreeSurfer. The signal-to-noise ratio (SNR) of the test MRI from a center does not look very good, but the FreeSurfer can analyze the gray matter. How much the allowable SNR for FreeSurfer analysis? This is the MRI protocol and the test image. Thank you in advance. Shujiro Siemens MAGNETOM Altea 1.5T Voxel size 1.0X1.0X1.0mm3 Geometry 　 FOV 256mm(256X256 matrix) Slice 176 Orientation sagittal Slice thickness 1mm Phase Encoding Dir A→P Timing 　 TR 2730 TI 1100 TE 1.64/3.59/5.36/7.31 bandwidth 651 RF 　 Magn.Preparation Non-sel.IR FA 7° Acceleration GRAPPA 　 Acceleration Factor PE 2 Reference Line PE 32 Slice Partial fourier 6/8 ScanTime 6:08 Shujiro Minami M.D., Ph.D. Dpt. of Otolaryngology National Tokyo Medical Center 2-5-1 Higashigaoka, Meguro, Tokyo 152-8902, Japan E-mail shujirominami(a)me.com

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Re: [Freesurfer] Freesurfer 7.1.0 on CentOS 8.1 {Disarmed}
by fsbuild 06 Nov '20

06 Nov '20

External Email - Use Caution Hello Ali, I would try using the RPM installer which should at least check some dependencies on X packages, system libraries, etc.,  https://secure-web.cisco.com/1QZVOusYuqG6pzgftW11woMO3J7wlOTz6CpOKDAkTB2PSK… - R. On Nov 5, 2020, at 22:39, Snedden, Ali <Ali.Snedden(a)nationwidechildrens.org> wrote:        External Email - Use Caution        Hello,  I’ve seen a couple mentions on the list-serv about difficulties using Freesurfer on CentOS 8.   My issue is likely similar, but I have a few more details.  I downloaded freesurfer-linux-centos8_x86_64-7.1.0.tar.gz.   When I launch `freeview`, it pops up a white/empty X window for a moment and then quickly disappears.   E.g. $ freeviewMESA-LOADER: failed to open swrast (search paths /usr/lib64/dri)libGL error: failed to load driver: swrastAborted (core dumped) I vaguely recall that the libGL errors _aren’t_ fatal.  I’ve seen them with other X applications.  Digging around the abort logs, I found the stack trace (see end of email).  Do you have thoughts on this?  I thought it might be a VTK compatibility issue, but that is a guess at best. Best regards,Ali  ###################### The stack trace ######################## [ccpp-2020-11-05-09:15:34-22241]# cat core_backtrace{   "signal": 6,   "executable": "/gpfs0/export/apps/opt/freesurfer/7.1.0/bin/freeview",   "only_crash_thread": true,   "stacktrace":      [ {   "crash_thread": true        ,   "frames":              [ {   "address": 140352624871839                ,   "build_id": "f796584f6ea7bb2e49cfd09412b9c6ec86eaf0fc"                ,   "build_id_offset": 227743                ,   "function_name": "raise"                ,   "file_name": "/usr/lib64/libc-2.28.so"                }              , {   "address": 140352624782581                ,   "build_id": "f796584f6ea7bb2e49cfd09412b9c6ec86eaf0fc"                ,   "build_id_offset": 138485                ,   "function_name": "abort"                ,   "file_name": "/usr/lib64/libc-2.28.so"                }              , {   "address": 140352824105729                ,   "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4"                ,   "build_id_offset": 1358593                ,   "function_name": "vtkXOpenGLRenderWindow::CreateAWindow()"                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"                }              , {   "address": 140352824102018                ,   "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4"                ,   "build_id_offset": 1354882                ,   "function_name": "vtkXOpenGLRenderWindow::WindowInitialize()"                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"                }              , {   "address": 140352824096013                ,   "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4"                ,   "build_id_offset": 1348877                ,   "function_name": "vtkXOpenGLRenderWindow::Start()"                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"                }              , {   "address": 140352717995302                ,   "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6"                ,   "build_id_offset": 1154342                ,   "function_name": "vtkRenderWindow::DoStereoRender()"                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1"                }              , {   "address": 140352717996715                ,   "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6"                ,   "build_id_offset": 1155755                ,   "function_name": "vtkRenderWindow::DoFDRender()"                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1"                }              , {   "address": 140352718000997                ,   "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6"                ,   "build_id_offset": 1160037                ,   "function_name": "vtkRenderWindow::DoAARender()"                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1"                }              , {   "address": 140352717997021                ,   "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6"                ,   "build_id_offset": 1156061                ,   "function_name": "vtkRenderWindow::Render()"                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1"                }              , {   "address": 140352824097713                ,   "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4"                ,   "build_id_offset": 1350577                ,   "function_name": "vtkXOpenGLRenderWindow::Render()"                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"                }              , {   "address": 5878611                ,   "build_id": "0de18d9e888c309c18e5e9450078f0fa6f19efa3"                ,   "build_id_offset": 1684307                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1..0/bin/freeview"                }              , {   "address": 140352637235160                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"                ,   "build_id_offset": 2695128                ,   "function_name": "QMetaObject::activate(QObject*, int, int, void**)"                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"                }              , {   "address": 140352637290759                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"                ,   "build_id_offset": 2750727                ,   "function_name": "QTimer::timeout(QTimer::QPrivateSignal)"                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"                }              , {   "address": 140352637291576                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"                ,   "build_id_offset": 2751544                ,   "function_name": "QTimer::timerEvent(QTimerEvent*)"                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"                }              , {   "address": 140352637241259                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"                ,   "build_id_offset": 2701227                ,   "function_name": "QObject::event(QEvent*)"                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"                }              , {   "address": 140352873383932                ,   "build_id": "ea0a04e7776bc525b6915e5ad0c369c06d3bcc24"                ,   "build_id_offset": 1447932                ,   "function_name": "QApplicationPrivate::notify_helper(QObject*, QEvent*)"                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Widgets.so.5"                }              , {   "address": 140352873412800                ,   "build_id": "ea0a04e7776bc525b6915e5ad0c369c06d3bcc24"                ,   "build_id_offset": 1476800                ,   "function_name": "QApplication::notify(QObject*, QEvent*)"                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Widgets.so.5"                }              , {   "address": 140352637064112                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"                ,   "build_id_offset": 2524080                ,   "function_name": "QCoreApplication::notifyInternal2(QObject*, QEvent*)"                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"                }              , {   "address": 140352637396158                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"                ,   "build_id_offset": 2856126                ,   "function_name": "QTimerInfoList::activateTimers()"                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"                }              , {   "address": 140352637398113                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"                ,   "build_id_offset": 2858081                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7..1.0/lib/qt/lib/libQt5Core.so.5"                }              , {   "address": 140352610068093                ,   "build_id": "2fa0454e76ccf97da64b0e34042c5e7470ed5328"                ,   "build_id_offset": 317053                ,   "function_name": "g_main_context_dispatch"                ,   "file_name": "/usr/lib64/libglib-2.0.so.0.5600.4"                }              , {   "address": 140352610069064                ,   "build_id": "2fa0454e76ccf97da64b0e34042c5e7470ed5328"                ,   "build_id_offset": 318024                ,   "function_name": "g_main_context_iterate.isra.21"                ,   "file_name": "/usr/lib64/libglib-2.0.so.0.5600.4"                }              , {   "address": 140352610069216                ,   "build_id": "2fa0454e76ccf97da64b0e34042c5e7470ed5328"                ,   "build_id_offset": 318176                ,   "function_name": "g_main_context_iteration"                ,   "file_name": "/usr/lib64/libglib-2.0.so.0.5600.4"                }              , {   "address": 140352637398919                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"                ,   "build_id_offset": 2858887                ,   "function_name": "QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>)"                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"                }              , {   "address": 140352570720945                ,   "build_id": "ef1892fde946d169edac88b08f41832db8acd8d7"                ,   "build_id_offset": 910001                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5XcbQpa.so.5"                }              , {   "address": 140352637057578                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"                ,   "build_id_offset": 2517546                ,   "function_name": "QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>)"                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"                }              , {   "address": 140352637092336                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"                ,   "build_id_offset": 2552304                ,   "function_name": "QCoreApplication::exec()"                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"                }              , {   "address": 4615883                ,   "build_id": "0de18d9e888c309c18e5e9450078f0fa6f19efa3"                ,   "build_id_offset": 421579                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/bin/freeview"                } ]        } ]} _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Freesurfer 7.1.0 on CentOS 8.1
by Snedden, Ali 05 Nov '20

05 Nov '20

External Email - Use Caution Hello, I’ve seen a couple mentions on the list-serv about difficulties using Freesurfer on CentOS 8. My issue is likely similar, but I have a few more details. I downloaded freesurfer-linux-centos8_x86_64-7.1.0.tar.gz. When I launch `freeview`, it pops up a white/empty X window for a moment and then quickly disappears. E.g. $ freeview MESA-LOADER: failed to open swrast (search paths /usr/lib64/dri) libGL error: failed to load driver: swrast Aborted (core dumped) I vaguely recall that the libGL errors _aren’t_ fatal. I’ve seen them with other X applications. Digging around the abort logs, I found the stack trace (see end of email). Do you have thoughts on this? I thought it might be a VTK compatibility issue, but that is a guess at best. Best regards, Ali ###################### The stack trace ######################## [ccpp-2020-11-05-09:15:34-22241]# cat core_backtrace { "signal": 6 , "executable": "/gpfs0/export/apps/opt/freesurfer/7.1.0/bin/freeview" , "only_crash_thread": true , "stacktrace": [ { "crash_thread": true , "frames": [ { "address": 140352624871839 , "build_id": "f796584f6ea7bb2e49cfd09412b9c6ec86eaf0fc" , "build_id_offset": 227743 , "function_name": "raise" , "file_name": "/usr/lib64/libc-2.28.so" } , { "address": 140352624782581 , "build_id": "f796584f6ea7bb2e49cfd09412b9c6ec86eaf0fc" , "build_id_offset": 138485 , "function_name": "abort" , "file_name": "/usr/lib64/libc-2.28.so" } , { "address": 140352824105729 , "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4" , "build_id_offset": 1358593 , "function_name": "vtkXOpenGLRenderWindow::CreateAWindow()" , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1" } , { "address": 140352824102018 , "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4" , "build_id_offset": 1354882 , "function_name": "vtkXOpenGLRenderWindow::WindowInitialize()" , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1" } , { "address": 140352824096013 , "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4" , "build_id_offset": 1348877 , "function_name": "vtkXOpenGLRenderWindow::Start()" , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1" } , { "address": 140352717995302 , "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6" , "build_id_offset": 1154342 , "function_name": "vtkRenderWindow::DoStereoRender()" , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1" } , { "address": 140352717996715 , "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6" , "build_id_offset": 1155755 , "function_name": "vtkRenderWindow::DoFDRender()" , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1" } , { "address": 140352718000997 , "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6" , "build_id_offset": 1160037 , "function_name": "vtkRenderWindow::DoAARender()" , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1" } , { "address": 140352717997021 , "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6" , "build_id_offset": 1156061 , "function_name": "vtkRenderWindow::Render()" , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1" } , { "address": 140352824097713 , "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4" , "build_id_offset": 1350577 , "function_name": "vtkXOpenGLRenderWindow::Render()" , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1" } , { "address": 5878611 , "build_id": "0de18d9e888c309c18e5e9450078f0fa6f19efa3" , "build_id_offset": 1684307 , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/bin/freeview" } , { "address": 140352637235160 , "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9" , "build_id_offset": 2695128 , "function_name": "QMetaObject::activate(QObject*, int, int, void**)" , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5" } , { "address": 140352637290759 , "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9" , "build_id_offset": 2750727 , "function_name": "QTimer::timeout(QTimer::QPrivateSignal)" , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5" } , { "address": 140352637291576 , "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9" , "build_id_offset": 2751544 , "function_name": "QTimer::timerEvent(QTimerEvent*)" , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5" } , { "address": 140352637241259 , "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9" , "build_id_offset": 2701227 , "function_name": "QObject::event(QEvent*)" , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5" } , { "address": 140352873383932 , "build_id": "ea0a04e7776bc525b6915e5ad0c369c06d3bcc24" , "build_id_offset": 1447932 , "function_name": "QApplicationPrivate::notify_helper(QObject*, QEvent*)" , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Widgets.so.5" } , { "address": 140352873412800 , "build_id": "ea0a04e7776bc525b6915e5ad0c369c06d3bcc24" , "build_id_offset": 1476800 , "function_name": "QApplication::notify(QObject*, QEvent*)" , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Widgets.so.5" } , { "address": 140352637064112 , "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9" , "build_id_offset": 2524080 , "function_name": "QCoreApplication::notifyInternal2(QObject*, QEvent*)" , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5" } , { "address": 140352637396158 , "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9" , "build_id_offset": 2856126 , "function_name": "QTimerInfoList::activateTimers()" , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5" } , { "address": 140352637398113 , "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9" , "build_id_offset": 2858081 , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5" } , { "address": 140352610068093 , "build_id": "2fa0454e76ccf97da64b0e34042c5e7470ed5328" , "build_id_offset": 317053 , "function_name": "g_main_context_dispatch" , "file_name": "/usr/lib64/libglib-2.0.so.0.5600.4" } , { "address": 140352610069064 , "build_id": "2fa0454e76ccf97da64b0e34042c5e7470ed5328" , "build_id_offset": 318024 , "function_name": "g_main_context_iterate.isra.21" , "file_name": "/usr/lib64/libglib-2.0.so.0.5600.4" } , { "address": 140352610069216 , "build_id": "2fa0454e76ccf97da64b0e34042c5e7470ed5328" , "build_id_offset": 318176 , "function_name": "g_main_context_iteration" , "file_name": "/usr/lib64/libglib-2.0.so.0.5600.4" } , { "address": 140352637398919 , "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9" , "build_id_offset": 2858887 , "function_name": "QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>)" , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5" } , { "address": 140352570720945 , "build_id": "ef1892fde946d169edac88b08f41832db8acd8d7" , "build_id_offset": 910001 , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5XcbQpa.so.5" } , { "address": 140352637057578 , "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9" , "build_id_offset": 2517546 , "function_name": "QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>)" , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5" } , { "address": 140352637092336 , "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9" , "build_id_offset": 2552304 , "function_name": "QCoreApplication::exec()" , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5" } , { "address": 4615883 , "build_id": "0de18d9e888c309c18e5e9450078f0fa6f19efa3" , "build_id_offset": 421579 , "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/bin/freeview" } ] } ] }

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Re: [Freesurfer] Welcome to the "Freesurfer" mailing list {Disarmed}
by fsbuild 05 Nov '20

05 Nov '20

External Email - Use Caution Hello Nicholas, Please check you setting for the environment variable FREESURFER_HOME.  I used the Mac 7.1.1 release package from https://secure-web.cisco.com/1UkHJYwewl8qS85O_CWV-J5WUiafp7vGnbHt… install freesurfer, so that means after installation FREESURFER_HOME is set as, $ export FREESURFER_HOME=/Applications/freesurfer/7.1.1 .... and the ls command outputs … $ ls $FREESURFER_HOMEASegStatsLUT.txt*              SetUpFreeSurfer.sh*            etc/                           sources.csh*DefectLUT.txt*                 Simple_surface_labels2009.txt* fsafd/                         sources.sh*FreeSurferColorLUT.txt*        WMParcStatsLUT.txt*            fsfast/                        subjects/FreeSurferEnv.csh*             average/                       lib/                           tkmeditParcColorsCMA*FreeSurferEnv.sh*              bin/                           matlab/                        trctrain/Freeview.app/                  build-stamp.txt*               mni/                           uninstall.sh*SegmentNoLUT.txt*              diffusion/                     python/SetUpFreeSurfer.csh*           docs/                          sessions/ … and shows the SetUpFreesurfer.sh script is there … Once you have set FREESURFER_HOME and verify with the ls command that you can see the SetUpFreesurfer.sh script, then it should work to do, $ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-darwin-macOS-7.1.1-20200726-8b40551 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.1.1FSFAST_HOME       /Applications/freesurfer/7.1.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.1.1/subjectsMNI_DIR           /Applications/freesurfer/7.1.1/mni There are instructions at https://secure-web.cisco.com/1yfyz92Kb9rfbFcHszgMJR0t3oQo4dtacsW4yW… the section "Using the Mac Package Installer” about using the installer package. - R. On Nov 4, 2020, at 22:58, Nicholas BH NG (NUHS) <nicholas_bh_ng(a)nuhs.edu.sg> wrote:        External Email - Use Caution        Dear Free SurferI followed the excellent video step by step instructions. At the last part of putting the code/ key into the terminal, I encountered the error message as below: no such file or directory. As such I think my set up was not complete.Kindly advice.Thank youNicholas Nicholass-MacBook-Pro:~ Nic$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-bash: /Applications/freesurfer/7.1.0/SetUpFreeSurfer.sh: No such file or directoryNicholass-MacBook-Pro:~ Nic$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-bash: /Applications/freesurfer/7.1.0/SetUpFreeSurfer.sh: No such file or directoryNicholass-MacBook-Pro:~ Nic$ Begin forwarded message:From: <freesurfer-request@nmr.mgh.harvard.edu>Subject: Welcome to the "Freesurfer" mailing listDate: 5 November 2020 at 11:56:45 AM SGTTo: <nicholas_bh_ng@nuhs.edu.sg>Email is from external source. Do not click on links or open files if unsure of sender..Welcome to the Freesurfer(a)nmr.mgh.harvard.edu mailing list!To post to this list, send your email to: freesurfer@nmr.mgh.harvard.eduGeneral information about the mailing list is at: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1U1Az2RL5IBE60ro0LKNRX0VzCwNbYE3pMJyje… you ever want to unsubscribe or change your options (eg, switch toor from digest mode, change your password, etc.), visit yoursubscription page at: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/19HZrRkjfKoxZblZuo0R6GPVxEHVP2CQHZavVh… can also make such adjustments via email by sending a message to: Freesurfer-request@nmr.mgh.harvard.eduwith the word `help' in the subject or body (don't include thequotes), and you will get back a message with instructions.You must know your password to change your options (including changingthe password, itself) or to unsubscribe.  It is: 3:5proverbsNormally, Mailman will remind you of your nmr.mgh.harvard..edu mailinglist passwords once every month, although you can disable this if youprefer.  This reminder will also include instructions on how tounsubscribe or change your account options.  There is also a button onyour options page that will email your current password to you.<p></p><image94f29b.PNG>MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1f9F22Nst6o56NQIQrR5eAr7N2En2k2SbYSUoiZ… Facebook | LinkedIn | VimeoImportant: This email and its attachments are confidential and may be privileged. If you are not the intended recipient, please notify the sender and delete it immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person without prior written permission. Thank you._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[FreeSurfer] Two Postdoctoral Fellowships in Aging and Alzheimer's disease {Disarmed}
by Hwamee Oh 05 Nov '20

05 Nov '20

External Email - Use Caution We are seeking two highly motivated postdoctoral researchers to lead NIH-funded projects in the Laboratory for Cognitive and Translational Neuroscience directed by Dr. Hwamee Oh at Brown University. One position is to use fMRI and PET to study visual memory networks in healthy young, cognitively normal older adults, and older adults who are considered as preclinical Alzheimer's disease. The other position is to understand the brain networks that underlie risk and resilience to aging and Alzheimer's disease in a 60-year longitudinal study cohort. Applicants with a Ph.D. degree in cognitive neuroscience, neuropsychology, biomedical engineering, or a relevant field are encouraged to apply. Prior experience with human neuroimaging, a strong background in cognitive neuroscience and experimental design, and/or familiarity with programming in relevant languages (e.g., Python, MATLAB) are required. The expected start date is July 2021 or negotiable. A link to the full description of the fellowship positions can be found here under "Research Fellowship Program": https://secure-web.cisco.com/1OPjthLpBzhYKFTSwjkVOmEIR06WelLxkClkKQkPxS4xR8… . A deadline for early decision applicants is December 11, 2020, and a regular decision deadline is January 4, 2021. More details can be found: https://secure-web.cisco.com/1nI5zbsgp-rII9YGTnQVPZOgDTWuOf1k9XnIzMiA-caXOK… . Interested applicants are strongly encouraged to email a brief description of research background and career goals, and CV with a list of 3 references to Dr. Hwamee Oh at hwamee_oh(a)brown.edu. Contact Website https://secure-web.cisco.com/1pnx_q2Y5nyTYo0Dg8xD1BekP2g7YWTdX_-COGIFVVfh7z…

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Different Sequences Longitudinal Stream {Disarmed}
by Backhausen, Lea 05 Nov '20

05 Nov '20

External Email - Use Caution Dear FreeSurfer experts, I am currently working on a longitudinal data set with 4 time points, acquired at one site with the same Siemens Trio 3T scanner. Unfourtunately, the T1 sequence differs slightly for one of these time points. These sequences have been measured: 1) repetition time (TR) = 2300 ms, echo time (TE) = 2.93 ms, inversion time (TI) = 900 ms, voxel size = 1.1 x 1.1 x 1.1mm, flip angle = 9°; matrix size = 256 x 256 x 160 mm 2) repetition time (TR) = 1900 ms, echo time (TE) = 2.26 ms, inversion time (TI) = 900 ms, voxel size = 1.0 x 1.0 x 1.0mm, flip angle = 9°; matrix size = 256 x 256 x 176 mm Is it possible to process these different sequences in the longitudinal stream (if e.g. one participant would have 3 data sets of sequence 1 and one data set of sequence 2)? Or would this cause too much bias? Thank you very much, kind regards! Lea Backhausen ------------------------------ Lea Backhausen Ph.D. Student (M.Sc. Psychology/Neuroscience) Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany http://secure-web.cisco.com/1uRUN3qw4_2ZQdVovG97ElQWo_5ofjkray9cxFwmREkCPYf…<http://secure-web.cisco.com/16jDYbTgO8Bi4O3L_8oBX-UxhLbIwNnO8u3tQFvD5bc-Ksr…>

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