Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

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

3 8

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

2 1

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": 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"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": 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"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…>

2 1

trac-preproc error
by Hasimoglu, Yasemin 05 Nov '20

05 Nov '20

Hi, I'm running Tracula on a longitudinal dataset and it's failing at the preproc stage for one subject with the following message: INFO: Distances between consecutive points in test subject's space are 16 13 12 14 WARN: Could not find satisfactory control point fit - try 4967 Finding center streamline INFO: Step is 3 voxels WARN: Turning off deviation check for center streamline INFO: Step is 3 voxels WARN: Turning off FA check for center streamline INFO: Step is 3 voxels WARN: Turning off overlap check for center streamline INFO: Step is 3 voxels WARN: All checks already off. Exiting. Selecting 5 points on center streamline ERROR: Selected streamline has fewer than 5 points Linux zorii.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Oct 28 04:11:51 EDT 2020 It looks like the problem is with one specific pathway. I checked the brainmask and the inter and intra-subject registrations and they all look fine to me, so I'm not sure what else to check. The trac-all.log file is quite large, I attempted to attach it in this email several times, but it always gets rejected, so I'm not attaching it for now. I would greatly appreciate any advice! Best, Yasemin

2 2

LGI quality control {Disarmed}
by Nelson, Eric 05 Nov '20

05 Nov '20

External Email - Use Caution Hello, I am using FreeSurfer 7.1.1 to run LGI and have done so successfully. I am now trying to quality check my data using tksurfer as described on the wiki tksurfer my_subject_id lh inflated -overlay lh.pial_lgi However the LGI overlay is not covering the entirety of the inflated brain. Specifically the medial frontal surface and some subcortical are not measured for LGI. Here is a link of the overlay images for a few subjects: https://secure-web.cisco.com/1FvGKanOWU0exqsmfZZWyCdCgTFgqf8kB2BXdsF-5A035k…. I<https://secure-web.cisco.com/1yytrZan4Ml7C4NJTkc91uplhrETEPm4MAwDFEYaEAXtVl…>. I haven't been able to find any images of what this overlay should look like so I don't know if this is expected or if something has gone wrong with the processing. Any feedback would be greatly appreciated Best, Eric

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