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30080 discussions

Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames!
by Knut J Bjuland 02 Mar '22

02 Mar '22

External Email - Use Caution Dear Freesurfer experts, I get this error when I am running FreeSurfer. Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /home/knutjb/subjects/test/mri/orig/001.mgz has 4 frames If this is a multi-frame MEMPRAGE image, use mri_concat --rms to combine echo frames. It has a t1_sag_mprage sequence, and it also give this waning filesare not found to be different and cannot be sorted. In addition, I get these errors when importing using recon-all -i file -all -s test INFO: Found 770 files in //20210224_151919/5_t1_sag_mprage INFO: Scanning for Series Number 5 Scanning Directory INFO: found 768 files in series INFO: loading series header info. When I am running mri_concat --rms I am able to run recon-all -all. Your sincerely, Knut Jørgen Bjuland

3 4

mri_binarize error when using trac-all -prep
by Thorn, Kathryn 02 Mar '22

02 Mar '22

External Email - Use Caution Hello Freesurfer Experts, I am currently attempting to process a single subject via Tracula v7.2. Previously, I used v6.0 to process this same dataset through all three steps of Tracula (prep, bedp, and path) with equivalent parameters with no errors. First, I ran recon-all -all on this subject which finished without error. Then I ran segmentThalamicNuclei.sh per instructions on the first page of the Tracula user guide - also finished without error. Then I passed the outputs of these steps onto trac-all -prep. tract-all -prep exits with errors after about a minute. The command is unable to find the file aparc+aseg+thalnuc.nii.gz. This traces back to an error with mri_binarize: mri_binarize --i /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/aparc+aseg.mgz --o /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz ERROR: must specify minimum and/or maximum threshold or match values aparc+aseg+thalnuc.nii.gz cannot be found because it is never created. However, all expected outputs previous to this file are created in the correct locations and trac-all -prep seems to be able to find all of the initial files I supply to it. I've attached the full trac-all -prep output as well as the config file I used for full context. Is there some threshold I need to specify in the config file? I looked at a complete example config file and I don't see any field related to this, but perhaps I'm missing something. Or is this perhaps due to some error in my data? Any ideas? Thank you! Kayti Thorn (she/her) Database Specialist Medical University of South Carolina Department of Neurology Center for Biomedical Imaging 135 Cannon St. CS101 Charleston, SC 29425

1 0

Linear mixed model for longitudinal data
by Julian Macoveanu 02 Mar '22

02 Mar '22

External Email - Use Caution Dear all, This is my first attempt to analyze longitudinal structural data with freesurfer, and I just do my best to follow the tutorial. I have some things not clear, so any help would be appreciated. We have a longitudinal study design with 2 groups, healthy and patients who were scanned at baseline a second time following a variable time interval (6 to 36 months). We want to investigate whether the patient’s cortical thickness/volume progresses differently compared to controls (group-by-time interaction effects). I chose to analyze the data with LME due to variable follow-up time, having only 50% of the patients with a second scan, and also having family members within and between groups. Questions 1) To account for familial relationship, should I add a family ID as covariate that stays in the design matrix X and count this covariate as random effect when the model is fitted? Like this: lhstats = lme_mass_fit_Rgw(X,[1 2 3],Y,ni,lhTh0,lhRgs,lhsphere); Where the first 3 covariates in X are counted as random effects: 1 the intercept, 2 follow-up time and 3 family ID. The X would further include group, age, sex, TIV, and group*time, the last one being the interaction term we want to assess using CM.C = [0 0 0 0 0 0 0 1]. Does the X and CM look good to address our research question? 2) It is unclear to me how to perform correction for multiple comparisons and assess what is significant. I follow this procedure after constructing X: [lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2 3],Y,ni,lhcortex,3); [lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere,lhRe,lhTh0,lhcortex,2,95); lhstats = lme_mass_fit_Rgw(X,[1 2 3],Y,ni,lhTh0,lhRgs,lhsphere); F_lhstats = lme_mass_F(lhstats,CM); dvtx = lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0): The dvtx is not empty but has 130 vertexes that survive. What I don’t understand, when constructing the sig.mgh map it appears the dvtx is not used: fs_write_fstats(F_lhstats,mri,'sig.mgh','sig'); How can I be sure when I import sig.mgh in Freeview I only look at the vertexes surviving multiple comparison? 3) Given a few clusters showing an interaction effect which are saved as sig.mgh and overlaid on surface in freeview, how do I know (visualize) what is going on in these clusters, like which of the group means go up or down? (I use FS71 and tksurfer not working). Is it here that printing out and plotting the betas (of the interaction term) are useful for? 4) I have a hypothesis to find differences in prefrontal cortex, at which step would I apply a PFC mask? I have constructed a PFC.label file by adding corresponding label files. Thank you, Julian

1 0

Re: [Freesurfer] Advice? Re: Freeview 7.1.1 won't start on Mac: segmentation fault
by fsbuild 02 Mar '22

02 Mar '22

External Email - Use Caution Hello Sam, While your crash report is from a Qt process (and not a WindowServer process), you might want to be aware there have been various reports of external monitors connected to Mac laptops causing crashes because the video hardware may not sense the correct resolution or refresh rate of external monitors through a USB-C to USB-C connection.  Some crashes were fixed by by using a USB-C (mac output) to HDMI (monitor input) connection.  Upgrading to Monterey apparently made things worse, https://secure-web.cisco.com/1DBOKcevsj0nBhREsCU8v_3geVkkvJnxbx… - R.. On Mar 1, 2022, at 23:08, Sam Buck Johnson <samjohns(a)stanford.edu> wrote:        External Email - Use Caution        Thanks very much Adam and Ruopeng,I believe that the external monitor was what was causing the error! Freeview seems to work normally now that I have detached it and am working only with my laptop's native display. I can only imagine how long it would have taken for me to discover this on my own.Thanks again,SamOn Mar 1, 2022, at 5:01 PM, Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:You can also download the latest build of freeview here:MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1p3g1aUfMpv-5OYWryXOH2Klul9BV737w-VN8f… Mar 1, 2022, at 7:44 PM, Adam Martersteck <acmarter(a)gmail.com> wrote:        External Email - Use Caution        Hi Sam,I can tell from your crash report you have a LG HDR 4K, 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) plugged in.You might try unplugging any external monitors and just having your native laptop display on then starting FreeView and seeing if it works.I had the same issue; see here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/10i4ZuCFZN8GuKB-DWCevEuF86X5PdpwHzWu9e… unresolved. Can open FreeView fine without a monitor plugged in but get a segmentation fault whenever I'm using an external display.-AdamOn Tue, Mar 1, 2022 at 4:04 PM Sam Buck Johnson <samjohns(a)stanford.edu> wrote:        External Email - Use Caution        Dear Freesurfer experts,I am writing to request technical assistance with freeview. I use freesurfer and freeview in my current research, where they are very valuable tools. However, upon upgrading my macbook's OS to macOS Monterey, Version 12.2.1, I now am unable to open freeview; it quits immediately upon starting. The error message indicates a segmentation fault, and in fact my error (and the error message) appears to be exactly the same as the one encountered by Alex White in this thread: https://secure-web.cisco.com/1IXdnFyTKmN2mh6oaF1iVQ3_Ho1Z9szlP… have been in correspondence with Alex, and he mentioned that you were able to help him resolve the issue, but that it required you to send him a patched version of freeview (or freesurfer?). I have the identical problem on freeview 7.1.1 and 7.2.0, but if possible I would prefer to continue working with your latest version, 7.2.0.Please do let me know if further information could help you understand this issue better. For the time being, I have copied the error message that prints to terminal and the full error report, both below.Any help/advice is much appreciated.Sincerely,Sam JohnsonPostdoctoral ScholarYeatman Brain and Education Lab, Stanford University GSE-----# terminal error message:(base) samjohns@DNab40bbcb 7.2.0 % freeview/Applications/freesurfer/7.2.0/bin/freeview: line 2:  1968 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"# full crash report-------------------------------------Translated Report (Full Report Below)-------------------------------------Process:               freeview [1673]Path:                  /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeviewIdentifier:            com.freesurfer.freeviewVersion:               ???Code Type:             X86-64 (Translated)Parent Process:        Exited process [1672]Responsible:           Terminal [1587]User ID:               502Date/Time:             2022-03-01 15:12:51.8713 -0800OS Version:            macOS 12.2.1 (21D62)Report Version:        12Anonymous UUID:        DCA45306-7159-2569-6BDE-CF94BEE1E522Time Awake Since Boot: 1200 secondsSystem Integrity Protection: enabledCrashed Thread:        0  Dispatch queue: com.apple.main-threadException Type:        EXC_BAD_ACCESS (SIGSEGV)Exception Codes:       KERN_INVALID_ADDRESS at 0x0000545845545f67Exception Codes:       0x0000000000000001, 0x0000545845545f67Exception Note:        EXC_CORPSE_NOTIFYTermination Reason:    Namespace SIGNAL, Code 11 Segmentation fault: 11Terminating Process:   exc handler [1673]VM Region Info: 0x545845545f67 is not in any region.  Bytes after previous region: 92257060675432  Bytes before following region: 12815019253913      REGION TYPE                    START - END         [ VSIZE] PRT/MAX SHRMOD  REGION DETAIL      commpage (reserved)        1000000000-7000000000   [384.0G] ---/--- SM=NUL  ...(unallocated)--->  GAP OF 0x5f9000000000 BYTES      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-/rwx SM=PRV  Thread 0 Crashed::  Dispatch queue: com.apple.main-thread0   freeview                                   0x104ec0ff8 0x104ce2000 + 19619761   QtWidgets                                  0x12046c6ed QWidget::event(QEvent*) + 11172   QtWidgets                                  0x12057dc45 QMainWindow::event(QEvent*) + 2773   QtWidgets                                  0x12043070d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 2694   QtWidgets                                  0x120431b12 QApplication::notify(QObject*, QEvent*) + 5945   QtCore                                     0x12266e564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 2126   QtWidgets                                  0x12048aa74 0x120420000 + 4368527   QtWidgets                                  0x12043070d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 2698   QtWidgets                                  0x120431b12 QApplication::notify(QObject*, QEvent*) + 5949   QtCore                                     0x12266e564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 21210  QtGui                                      0x1211e2a74 QGuiApplicationPrivate::processGeometryChangeEvent(QWindowSystemInterfacePrivate::GeometryChangeEvent*) + 51611  QtGui                                      0x1211e3420 QGuiApplicationPrivate::processWindowScreenChangedEvent(QWindowSystemInterfacePrivate::WindowScreenChangedEvent*) + 73612  QtGui                                      0x1211c1c33 bool QWindowSystemInterfacePrivate::handleWindowSystemEvent<QWindowSystemInterface::SynchronousDelivery>(QWindowSystemInterfacePrivate::WindowSystemEvent*) + 11513  libqcocoa.dylib                            0x121eb4c77 0x121e96000 + 12607114  libqcocoa.dylib                            0x121eae862 0x121e96000 + 10045015  libqcocoa.dylib                            0x121eae2eb 0x121e96000 + 9905116  QtGui                                      0x1211ec1dc QWindowPrivate::create(bool, unsigned long long) + 14017  QtWidgets                                  0x120459e31 QWidgetPrivate::create() + 120118  QtWidgets                                  0x120458b22 QWidget::create(unsigned long long, bool, bool) + 32219  QtWidgets                                  0x12057e4d7 QMainWindow::setUnifiedTitleAndToolBarOnMac(bool) + 5520  freeview                                   0x104eaf497 0x104ce2000 + 188943121  freeview                                   0x104ea950e 0x104ce2000 + 186497422  freeview                                   0x104de279a 0x104ce2000 + 105052223  dyld                                       0x2158184fe start + 462Thread 1:: com.apple..rosetta.exceptionserver0   runtime                                 0x7ff7ffc578e4 0x7ff7ffc53000 + 186601   runtime                                 0x7ff7ffc64928 0x7ff7ffc53000 + 719762   runtime                                 0x7ff7ffc660a4 0x7ff7ffc53000 + 77988Thread 2:0   runtime                                 0x7ff7ffc75814 0x7ff7ffc53000 + 141332Thread 3:0   runtime                                 0x7ff7ffc75814 0x7ff7ffc53000 + 141332Thread 4::  Dispatch queue: com.apple.dock.fullscreen0   dyld                                       0x215824e0c dyld4::Loader::LoaderRef::loader(dyld4::RuntimeState const&) const + 681   dyld                                       0x21582cdb1 dyld4::PrebuiltLoader::dependent(dyld4::RuntimeState const&, unsigned int, dyld4::Loader::DependentKind*) const + 952   dyld                                       0x215828a1e dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 5323   dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 5934   dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 5935   dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 5936   dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 5937   dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 5938   dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 5939   dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 59310  dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 59311  dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 59312  dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 59313  dyld                                       0x215837b4c dyld4::APIs::dlsym(void*, char const*) + 65614  SkyLight                                0x7ff811fbf581 __loginframework_vtable_block_invoke + 60515  libdispatch.dylib                       0x7ff80ccd8cc9 _dispatch_client_callout + 816  libdispatch.dylib                       0x7ff80ccd9ec1 _dispatch_once_callout + 2017  SkyLight                                0x7ff811fc0de5 SLSCopyCurrentSessionPropertiesInternalBridge + 36618  SkyLight                                0x7ff811e6a097 SLSessionCopyCurrentDictionary + 1219  AppKit                                  0x7ff80f9e04ee -[NSDockConnection _makeConnectionIfNeededWithRetryInterval:onDemand:] + 4720  AppKit                                  0x7ff8101b9720 __35-[NSDockConnection startConnection]_block_invoke.37 + 4521  libdispatch.dylib                       0x7ff80ccd7ad8 _dispatch_call_block_and_release + 1222  libdispatch.dylib                       0x7ff80ccd8cc9 _dispatch_client_callout + 823  libdispatch.dylib                       0x7ff80ccdecee _dispatch_lane_serial_drain + 69624  libdispatch.dylib                       0x7ff80ccdf7c8 _dispatch_lane_invoke + 36625  libdispatch.dylib                       0x7ff80cce97e1 _dispatch_workloop_worker_thread + 75826  libsystem_pthread.dylib                 0x7ff80ce8f074 _pthread_wqthread + 32627  libsystem_pthread.dylib                 0x7ff80ce8dffb start_wqthread + 15Thread 5:0   runtime                                 0x7ff7ffc75814 0x7ff7ffc53000 + 141332Thread 6:0   runtime                                 0x7ff7ffc75814 0x7ff7ffc53000 + 141332Thread 7:0   runtime                                 0x7ff7ffc75814 0x7ff7ffc53000 + 141332Thread 0 crashed with X86 Thread State (64-bit):  rax: 0x0000545845545f5f  rbx: 0x000000031e5aac00  rcx: 0x0000000000010000  rdx: 0x000000012046c6dd  rdi: 0x00007ff815d4f000  rsi: 0x000000031e5a9c78  rbp: 0x000000031e5a9730  rsp: 0x000000031e5a9720   r8: 0x0000000000000000   r9: 0x0000000000000000  r10: 0x00000001220129e0  r11: 0x00007ff80f8c8bb9  r12: 0x00007ff175745090  r13: 0x000000031e5aac00  r14: 0x000000031e5a9c78  r15: 0x000000031e5a9c78  rip: 0x0000000104ec0ff8  rfl: 0x0000000000000203 tmp0: 0x0000000115a9c01c tmp1: 0x000000012046c6ed tmp2: 0x0000000120a3c1e8Binary Images:       0x104ce2000 -        0x106349fff com.freesurfer.freeview (*) <35cc1656-e7ff-32a5-8ec9-9faf896f9915> /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview       0x120420000 -        0x12085efff org.qt-project.QtWidgets (5.12) <ef671b84-7965-3c74-89df-09c3fa9096ca> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtWidgets.framework/Versions/5/QtWidgets       0x122484000 -        0x1229b9fff org.qt-project.QtCore (5.12) <ae294ca9-b3ec-3f0e-b67a-509a13c0c913> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtCore.framework/Versions/5/QtCore       0x1211ac000 -        0x1215f8fff org.qt-project.QtGui (5.12) <9cc34b01-ae4a-3ff2-ac1b-de08b8fbbbae> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtGui.framework/Versions/5/QtGui       0x121e96000 -        0x121ffcfff libqcocoa.dylib (*) <14bc2336-68e6-3ace-b3a9-f21152a64785> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/platforms/libqcocoa.dylib       0x215813000 -        0x21587efff dyld (*) <7de33963-bbc5-3996-ba6e-f1d562c17c95> /usr/lib/dyld    0x7ff7ffc53000 -     0x7ff7ffc82fff runtime (*) <faca02c7-0a4c-3629-a746-55ddcfee9116> /usr/libexec/rosetta/runtime    0x7ff811d55000 -     0x7ff8120eafff com.apple.SkyLight (1.600.0) <eab4373e-52ca-38d7-963a-9f5bd71824e9> /System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/SkyLight    0x7ff80ccd6000 -     0x7ff80cd1cfff libdispatch.dylib (*) <67d92c93-aa68-34c2-964b-23e8a8d32098> /usr/lib/system/libdispatch.dylib    0x7ff80f86e000 -     0x7ff8106fffff com.apple.AppKit (6.9) <9d3ab204-4858-3120-b002-5c38b02edec4> /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit    0x7ff80ce8c000 -     0x7ff80ce97fff libsystem_pthread.dylib (*) <ee564342-d8f2-396d-b642-40092cf34d82> /usr/lib/system/libsystem_pthread.dylib               0x0 - 0xffffffffffffffff ??? (*) <00000000-0000-0000-0000-000000000000> ???External Modification Summary:  Calls made by other processes targeting this process:    task_for_pid: 0    thread_create: 0    thread_set_state: 0  Calls made by this process:    task_for_pid: 0    thread_create: 0    thread_set_state: 0  Calls made by all processes on this machine:    task_for_pid: 0    thread_create: 0    thread_set_state: 0VM Region Summary:ReadOnly portion of Libraries: Total=964.1M resident=0K(0%) swapped_out_or_unallocated=964.1M(100%)Writable regions: Total=1.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.2G(100%)                                VIRTUAL   REGION REGION TYPE                        SIZE    COUNT (non-coalesced) ===========                     =======  ======= Accelerate framework               256K        2 Activity Tracing                   256K        1 CG backing stores                 5056K        8 ColorSync                          228K       25 CoreGraphics                    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 reserved VM address space (unallocated)__DATA                           262.5M      320 __DATA_CONST                      12.2M      173 __DATA_DIRTY                       539K       99 __FONT_DATA                          4K        1 __LINKEDIT                       704.8M       29 __OBJC_RO                         81.8M        1 __OBJC_RW                         3136K        2 __TEXT                           259.3M      332 __UNICODE                          588K        1 dyld private memory               1024K        1 mapped file                        5.1G      429 shared memory                      848K       22 unshared pmap                     5504K        3 ===========                     =======  ======= TOTAL                              7.4G     1749 TOTAL, minus reserved VM space     6.8G     1749 -----------Full Report-----------{"app_name":"freeview","timestamp":"2022-03-01 15:12:52.00 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"bundleInfo" : {"CFBundleIdentifier":"com.freesurfer.freeview"},  "storeInfo" : {"deviceIdentifierForVendor":"61B48C8D-0860-568E-953B-3DE776CD3C66","thirdParty":true},  "parentProc" : "Exited process",  "parentPid" : 1672,  "coalitionName" : "com.apple.Terminal",  "crashReporterKey" : "DCA45306-7159-2569-6BDE-CF94BEE1E522",  "responsiblePid" : 1587,  "responsibleProc" : "Terminal",  "sip" : "enabled",  "vmRegionInfo" : "0x545845545f67 is not in any region.  Bytes after previous region: 92257060675432  Bytes before following region: 12815019253913\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",  "isCorpse" : 1,  "exception" : {"codes":"0x0000000000000001, 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 REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               256K        2 \nActivity Tracing                   256K        1 \nCG backing stores                 5056K        8 \nColorSync                          228K       25 \nCoreGraphics                         8K        2 \nCoreUI image data                  152K        1 \nFoundation                          16K        1 \nKernel Alloc Once                    8K        1 \nMALLOC                           216.2M       34 \nMALLOC guard page                  192K        9 \nMALLOC_MEDIUM (reserved)         240.0M        2         reserved VM address space (unallocated) \nMALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)\nRosetta Arena                     4096K        2 \nRosetta Generic                    736K      181 \nRosetta IndirectBranch             512K        1 \nRosetta JIT                      128.0M        1 \nRosetta Return Stack               100K       10 \nRosetta Thread Context             100K       10 \nSTACK GUARD                         20K        5 \nStack                             11.1M        7 \nStack Guard                       56.0M        2 \nVM_ALLOCATE                       8280K       29 \nVM_ALLOCATE (reserved)               4K        1         reserved VM address space (unallocated)\n__DATA                           262.5M      320 \n__DATA_CONST                      12.2M      173 \n__DATA_DIRTY                       539K       99 \n__FONT_DATA                          4K        1 \n__LINKEDIT                       704.8M       29 \n__OBJC_RO                          81.8M        1 \n__OBJC_RW                  !        3136K        2 \n__TEXT                           259.3M      332 \n__UNICODE                          588K        1 \ndyld private memory               1024K        1 \nmapped file                        5.1G      429 \nshared memory                      848K       22 \nunshared pmap                     5504K        3 \n===========                     =======  ======= \nTOTAL                              7.4G     1749 \nTOTAL, minus reserved VM space     6.8G     1749 \n",  "legacyInfo" : {  "threadTriggered" : {    "queue" : "com.apple.main-thread"  }},  "trialInfo" : {  "rollouts" : [    {      "rolloutId" : "5fc94383418129005b4e9ae0",      "factorPackIds" : {      },      "deploymentId" : 240000252    },    {      "rolloutId" : "5ffde50ce2aacd000d47a95f",      "factorPackIds" : {      },      "deploymentId" : 240000111    },    {      "rolloutId" : "601d9415f79519000ccd4b69",      "factorPackIds" : {        "SIRI_TEXT_TO_SPEECH" : "620161cb295c182621eced20"      },      "deploymentId" : 240000392    },    {      "rolloutId" : "602ad4dac86151000cf27e46",      "factorPackIds" : {        "SIRI_DICTATION_ASSETS" : "61fb0e87c773c43cde3bb80e"      },      "deploymentId" : 240000305    },    {      "rolloutId" : "60da5e84ab0ca017dace9abf",      "factorPackIds" : {      },      "deploymentId" : 240000008    },    {      "rolloutId" : "607844aa04477260f58a8077",      "factorPackIds" : {        "SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"      },      "deploymentId" : 240000066    }  ],  "experiments" : [  ]}}Model: MacBookPro17,1, BootROM 7429.81.3, proc 8:4:4 processors, 16 GB, SMC Graphics: Apple M1, Apple M1, Built-InDisplay: Color LCD, 2560 x 1600 Retina, Main, MirrorOff, OnlineDisplay: LG HDR 4K, 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition), MirrorOff, OnlineMemory Module: LPDDR4AirPort: Wi-Fi, wl0: Oct 26 2021 16:10:41 version 18.20.310.15.7.8.120 FWID 01-5d6c3867Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial portsNetwork Service: USB 10/100/1000 LAN, Ethernet, en6Network Service: Wi-Fi, AirPort, en0USB Device: USB31BusUSB Device: hub_deviceUSB Device: USB ReceiverUSB Device: USB ControlsUSB Device: USB31BusUSB Device: USB 10/100/1000 LANThunderbolt Bus: MacBook Pro, Apple Inc.Thunderbolt Bus: MacBook Pro, Apple Inc._______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1UFwUOZVxJzNHib_BUcrO5B5fE0pXfoxNaO6Sj… information in this e-mail is intended only for the person to whom it is addressed.  If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://http://secure-web.cisco.com/1fMqjQ6tptzVpGnw_jgJYR3sLftZO8hm-LN7O… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://www..massgeneralbrigham.org/complianceline> .Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over 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1 0

Advice? Re: Freeview 7.1.1 won't start on Mac: segmentation fault
by Sam Buck Johnson 01 Mar '22

01 Mar '22

External Email - Use Caution Dear Freesurfer experts, I am writing to request technical assistance with freeview. I use freesurfer and freeview in my current research, where they are very valuable tools. However, upon upgrading my macbook's OS to macOS Monterey, Version 12.2.1, I now am unable to open freeview; it quits immediately upon starting. The error message indicates a segmentation fault, and in fact my error (and the error message) appears to be exactly the same as the one encountered by Alex White in this thread: https://secure-web.cisco.com/1IXdnFyTKmN2mh6oaF1iVQ3_Ho1Z9szlPmaAOZrSIy7EZw… I have been in correspondence with Alex, and he mentioned that you were able to help him resolve the issue, but that it required you to send him a patched version of freeview (or freesurfer?). I have the identical problem on freeview 7.1.1 and 7.2.0, but if possible I would prefer to continue working with your latest version, 7.2.0. Please do let me know if further information could help you understand this issue better. For the time being, I have copied the error message that prints to terminal and the full error report, both below. Any help/advice is much appreciated. Sincerely, Sam Johnson Postdoctoral Scholar Yeatman Brain and Education Lab, Stanford University GSE ----- # terminal error message: (base) samjohns@DNab40bbcb 7.2.0 % freeview /Applications/freesurfer/7.2.0/bin/freeview: line 2: 1968 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" # full crash report ------------------------------------- Translated Report (Full Report Below) ------------------------------------- Process: freeview [1673] Path: /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview Identifier: com.freesurfer.freeview Version: ??? Code Type: X86-64 (Translated) Parent Process: Exited process [1672] Responsible: Terminal [1587] User ID: 502 Date/Time: 2022-03-01 15:12:51.8713 -0800 OS Version: macOS 12.2.1 (21D62) Report Version: 12 Anonymous UUID: DCA45306-7159-2569-6BDE-CF94BEE1E522 Time Awake Since Boot: 1200 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 0x0000545845545f67 Exception Codes: 0x0000000000000001, 0x0000545845545f67 Exception Note: EXC_CORPSE_NOTIFY Termination Reason: Namespace SIGNAL, Code 11 Segmentation fault: 11 Terminating Process: exc handler [1673] VM Region Info: 0x545845545f67 is not in any region. Bytes after previous region: 92257060675432 Bytes before following region: 12815019253913 REGION TYPE START - END [ VSIZE] PRT/MAX SHRMOD REGION DETAIL commpage (reserved) 1000000000-7000000000 [384.0G] ---/--- SM=NUL ...(unallocated) ---> GAP OF 0x5f9000000000 BYTES MALLOC_NANO 600000000000-600008000000 [128.0M] rw-/rwx SM=PRV Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 freeview 0x104ec0ff8 0x104ce2000 + 1961976 1 QtWidgets 0x12046c6ed QWidget::event(QEvent*) + 1117 2 QtWidgets 0x12057dc45 QMainWindow::event(QEvent*) + 277 3 QtWidgets 0x12043070d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 4 QtWidgets 0x120431b12 QApplication::notify(QObject*, QEvent*) + 594 5 QtCore 0x12266e564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 6 QtWidgets 0x12048aa74 0x120420000 + 436852 7 QtWidgets 0x12043070d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 8 QtWidgets 0x120431b12 QApplication::notify(QObject*, QEvent*) + 594 9 QtCore 0x12266e564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 10 QtGui 0x1211e2a74 QGuiApplicationPrivate::processGeometryChangeEvent(QWindowSystemInterfacePrivate::GeometryChangeEvent*) + 516 11 QtGui 0x1211e3420 QGuiApplicationPrivate::processWindowScreenChangedEvent(QWindowSystemInterfacePrivate::WindowScreenChangedEvent*) + 736 12 QtGui 0x1211c1c33 bool QWindowSystemInterfacePrivate::handleWindowSystemEvent<QWindowSystemInterface::SynchronousDelivery>(QWindowSystemInterfacePrivate::WindowSystemEvent*) + 115 13 libqcocoa.dylib 0x121eb4c77 0x121e96000 + 126071 14 libqcocoa.dylib 0x121eae862 0x121e96000 + 100450 15 libqcocoa.dylib 0x121eae2eb 0x121e96000 + 99051 16 QtGui 0x1211ec1dc QWindowPrivate::create(bool, unsigned long long) + 140 17 QtWidgets 0x120459e31 QWidgetPrivate::create() + 1201 18 QtWidgets 0x120458b22 QWidget::create(unsigned long long, bool, bool) + 322 19 QtWidgets 0x12057e4d7 QMainWindow::setUnifiedTitleAndToolBarOnMac(bool) + 55 20 freeview 0x104eaf497 0x104ce2000 + 1889431 21 freeview 0x104ea950e 0x104ce2000 + 1864974 22 freeview 0x104de279a 0x104ce2000 + 1050522 23 dyld 0x2158184fe start + 462 Thread 1:: com.apple.rosetta.exceptionserver 0 runtime 0x7ff7ffc578e4 0x7ff7ffc53000 + 18660 1 runtime 0x7ff7ffc64928 0x7ff7ffc53000 + 71976 2 runtime 0x7ff7ffc660a4 0x7ff7ffc53000 + 77988 Thread 2: 0 runtime 0x7ff7ffc75814 0x7ff7ffc53000 + 141332 Thread 3: 0 runtime 0x7ff7ffc75814 0x7ff7ffc53000 + 141332 Thread 4:: Dispatch queue: com.apple.dock.fullscreen 0 dyld 0x215824e0c dyld4::Loader::LoaderRef::loader(dyld4::RuntimeState const&) const + 68 1 dyld 0x21582cdb1 dyld4::PrebuiltLoader::dependent(dyld4::RuntimeState const&, unsigned int, dyld4::Loader::DependentKind*) const + 95 2 dyld 0x215828a1e dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 532 3 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 4 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 5 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 6 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 7 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 8 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 9 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 10 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 11 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 12 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 13 dyld 0x215837b4c dyld4::APIs::dlsym(void*, char const*) + 656 14 SkyLight 0x7ff811fbf581 __loginframework_vtable_block_invoke + 605 15 libdispatch.dylib 0x7ff80ccd8cc9 _dispatch_client_callout + 8 16 libdispatch.dylib 0x7ff80ccd9ec1 _dispatch_once_callout + 20 17 SkyLight 0x7ff811fc0de5 SLSCopyCurrentSessionPropertiesInternalBridge + 366 18 SkyLight 0x7ff811e6a097 SLSessionCopyCurrentDictionary + 12 19 AppKit 0x7ff80f9e04ee -[NSDockConnection _makeConnectionIfNeededWithRetryInterval:onDemand:] + 47 20 AppKit 0x7ff8101b9720 __35-[NSDockConnection startConnection]_block_invoke.37 + 45 21 libdispatch.dylib 0x7ff80ccd7ad8 _dispatch_call_block_and_release + 12 22 libdispatch.dylib 0x7ff80ccd8cc9 _dispatch_client_callout + 8 23 libdispatch.dylib 0x7ff80ccdecee _dispatch_lane_serial_drain + 696 24 libdispatch.dylib 0x7ff80ccdf7c8 _dispatch_lane_invoke + 366 25 libdispatch.dylib 0x7ff80cce97e1 _dispatch_workloop_worker_thread + 758 26 libsystem_pthread.dylib 0x7ff80ce8f074 _pthread_wqthread + 326 27 libsystem_pthread.dylib 0x7ff80ce8dffb start_wqthread + 15 Thread 5: 0 runtime 0x7ff7ffc75814 0x7ff7ffc53000 + 141332 Thread 6: 0 runtime 0x7ff7ffc75814 0x7ff7ffc53000 + 141332 Thread 7: 0 runtime 0x7ff7ffc75814 0x7ff7ffc53000 + 141332 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000545845545f5f rbx: 0x000000031e5aac00 rcx: 0x0000000000010000 rdx: 0x000000012046c6dd rdi: 0x00007ff815d4f000 rsi: 0x000000031e5a9c78 rbp: 0x000000031e5a9730 rsp: 0x000000031e5a9720 r8: 0x0000000000000000 r9: 0x0000000000000000 r10: 0x00000001220129e0 r11: 0x00007ff80f8c8bb9 r12: 0x00007ff175745090 r13: 0x000000031e5aac00 r14: 0x000000031e5a9c78 r15: 0x000000031e5a9c78 rip: 0x0000000104ec0ff8 rfl: 0x0000000000000203 tmp0: 0x0000000115a9c01c tmp1: 0x000000012046c6ed tmp2: 0x0000000120a3c1e8 Binary Images: 0x104ce2000 - 0x106349fff com.freesurfer.freeview (*) <35cc1656-e7ff-32a5-8ec9-9faf896f9915> /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview 0x120420000 - 0x12085efff org.qt-project.QtWidgets (5.12) <ef671b84-7965-3c74-89df-09c3fa9096ca> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtWidgets.framework/Versions/5/QtWidgets 0x122484000 - 0x1229b9fff org.qt-project.QtCore (5.12) <ae294ca9-b3ec-3f0e-b67a-509a13c0c913> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtCore.framework/Versions/5/QtCore 0x1211ac000 - 0x1215f8fff org.qt-project.QtGui (5.12) <9cc34b01-ae4a-3ff2-ac1b-de08b8fbbbae> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtGui.framework/Versions/5/QtGui 0x121e96000 - 0x121ffcfff libqcocoa.dylib (*) <14bc2336-68e6-3ace-b3a9-f21152a64785> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/platforms/libqcocoa.dylib 0x215813000 - 0x21587efff dyld (*) <7de33963-bbc5-3996-ba6e-f1d562c17c95> /usr/lib/dyld 0x7ff7ffc53000 - 0x7ff7ffc82fff runtime (*) <faca02c7-0a4c-3629-a746-55ddcfee9116> /usr/libexec/rosetta/runtime 0x7ff811d55000 - 0x7ff8120eafff com.apple.SkyLight (1.600.0) <eab4373e-52ca-38d7-963a-9f5bd71824e9> /System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/SkyLight 0x7ff80ccd6000 - 0x7ff80cd1cfff libdispatch.dylib (*) <67d92c93-aa68-34c2-964b-23e8a8d32098> /usr/lib/system/libdispatch.dylib 0x7ff80f86e000 - 0x7ff8106fffff com.apple.AppKit (6.9) <9d3ab204-4858-3120-b002-5c38b02edec4> /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit 0x7ff80ce8c000 - 0x7ff80ce97fff libsystem_pthread.dylib (*) <ee564342-d8f2-396d-b642-40092cf34d82> /usr/lib/system/libsystem_pthread.dylib 0x0 - 0xffffffffffffffff ??? (*) <00000000-0000-0000-0000-000000000000> ??? 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Thunderbolt Bus: MacBook Pro, Apple Inc.

3 3

Re: [Freesurfer] SAMSEG "lesion" (Illegal instruction) ~ running VM_67
by Cerri, Stefano 28 Feb '22

28 Feb '22

Hi Randy, Your run_samseg syntax is correct and yes, the "lesion" version of SAMSEG requires Tensorflow. The "illegal instruction" error is most probably related to an incompatible version of Tensorflow with your CPU instruction set. You should be able to replicate the error by typing: 1. fspython 1. import tensorflow Would you be able to run SAMSEG lesion on another host machine (possibly a relatively new one) and let us know if the error persists? Best, Stefano Dear R, Yes, I have tried to run "samseg_run" from the command line (I've repeated my syntax below).? I have looked both under the directory where the command ran that produced the ?Illegal instruction? error.? No crash file (a logfile?) or a "core" file were written.? I also looked?/var/crash but that folder was empty too. As I mentioned, I'm a LINUX novice.? I'm even more of a novice with regard to Python. However, I did take a quick at the code looking for any mention of tensorflow, and have copied the python script text as it exists below.? I have highlighted the only mention of tensorflow below.? Does this look like you expect it? Has tensorflow actually been incorporated into the VM??? Note that I have been able to successfully run Samseg without the --lesion flag and the process works just fine (about 20min runtime, aseg looks just fine in Freeview) Again, thanks for any guidance you can provide. -Randy xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx #!/usr/bin/env python import osimport sysimport jsonimport scipy.ioimport freesurfer as fsimport freesurfer.samseg as samseg # ------ Parse Command Line Arguments ------ parser = fs.utils.ArgumentParser() default_threads = int(os.environ.get('OMP_NUM_THREADS', 1)) # requiredparser.add_argument('-o', '--output', metavar='DIR', dest='outputDirectory', help='Output directory.', required=True)parser.add_argument('-i', '--input', nargs='+', action='extend', metavar='FILE', dest='inputFileNames', help='Input image(s).', required=True)# optional processing optionsparser.add_argument('-m', '--mode', nargs='+', help='Output basenames for the input image mode.')parser.add_argument('--threads', type=int, default=default_threads, help='Number of threads to use. Defaults to current OMP_NUM_THREADS or 1.')parser.add_argument('--reg-only', action='store_true', default=False, help='Only perform initial affine registration.')parser.add_argument('-r', '--reg', metavar='FILE', help='Skip initial affine registration and read transform from file.')parser.add_argument('--init-reg', metavar='FILE', help='Initial affine registration.')parser.add_argument('-a', '--atlas', metavar='DIR', help='Point to an alternative atlas directory.')parser.add_argument('--gmm', metav ar='FILE', help='Point to an alternative GMM file.')parser.add_argument('--ignore-unknown', action='store_true', help='Ignore final priors corresponding to unknown class.')parser.add_argument('--options', metavar='FILE', help='Override advanced options via a json file.')parser.add_argument('--pallidum-separate', action='store_true', default=False, help='Move pallidum outside of global white matter class. Use this flag when T2/flair is used.')# optional lesion optionsparser.add_argument('--lesion', action='store_true', default=False, help='Enable lesion segmentation (requires tensorflow).')parser.add_argument('--threshold', type=float, default=0.3, help='Lesion threshold for final segmentation. Lesion segmentation must be enabled.')parser.add_argument('--samples', type=int, default=50, help='Number of samples for lesion segmentation. Lesion segmentation must be enabled.')parser.add_argument('--burnin', type=int, default=50, help='Number of burn-in samples for lesion segmentation. Les ion segmentation must be enabled.')parser.ad! d_argume nt('--lesion-pseudo-samples', nargs=2, type=float, default=[500, 500], help='Lesion pseudo samples mean and variance.')parser.add_argument('--lesion-rho', type=float, default=50, help='Lesion ratio.')parser.add_argument('--lesion-mask-structure', default='Cortex', help='Intensity mask brain structure. Lesion segmentation must be enabled.')parser.add_argument('--lesion-mask-pattern', type=int, nargs='+', help='Lesion mask list (set value for each input volume): -1 below lesion mask structure mean, +1 above, 0 no mask. Lesion segmentation must be enabled.')# optional debugging optionsparser.add_argument('--history', action='store_true', default=False, help='Save history.')parser.add_argument('--save-posteriors', nargs='*', help='Save posterior volumes to the "posteriors" subdirectory.')parser.add_argument('--save-probabilities', action='store_true', help='Save final modal class probabilities to "probabilities" subdirectory.')parser.add_argument('--showfigs', action='store_true', defaul t=False, help='Show figures during run.')parser.add_argument('--save-mesh', action='store_true', help='Save the final mesh in template space.')parser.add_argument('--save-warp', action='store_true', help='Save the image->template warp field.')parser.add_argument('--movie', action='store_true', default=False, help='Show history as arrow key controlled time sequence.') args = parser.parse_args() # ------ Initial Setup ------ # Make sure freesurfer has been sourcedif not fs.fshome():? ? fs.fatal('FREESURFER_HOME must be set') # Start the process timertimer = fs.utils.Timer() # Create the output folderos.makedirs(args.outputDirectory, exist_ok=True) # Specify the maximum number of threads the GEMS code will usesamseg.setGlobalDefaultNumberOfThreads(args.threads) # Remove previous cost logcostfile = os.path.join(args.outputDirectory, 'cost.txt')if os.path.exists( costfile ):? ? os.remove( costfile )? # Get the atlas directoryatlasDir = os.environ.get('SAMSEG_DATA_DIR')if args.atlas:? ? atlasDir = args.atlasif not atlasDir:? ? # Altas defaults? ? if args.lesion:? ? ? ? defaultAtlas = '20Subjects_smoothing2_down2_smoothingForAffine2_lesion'? ? else:? ? ? ? defaultAtlas = '20Subjects_smoothing2_down2_smoothingForAffine2'? ? atlasDir = os.path.join(fs.fshome(), 'average', 'samseg', defaultAtlas) # Setup the visualization toolvisualizer = samseg.initVisualizer(args.showfigs, args.movie) # ------ Prepare Samseg Parameters ------ # Load user options from a JSON fileuserModelSpecifications = {}userOptimizationOptions = {}if args.options:? ? with open(args.options) as f:? ? ? ? userOptions = json.load(f)? ? if userOptions.get('modelSpecifications') is not None:?? ? ? ? userModelSpecifications = userOptions.get('modelSpecifications')? ? if userOptions.get('optimizationOptions') is not None:?? ? ? ? userOptimizationOptions = userOptions.get('optimizationOptions') # Check if --save-posteriors was specified without any structure search stringif args.save_posteriors is not None and len(args.save_posteriors) == 0:? ? savePosteriors = Trueelse:? ? savePosteriors = args.save_posteriors # ------ Run Samseg ------ samseg_kwargs = dict(? ? imageFileNames=args.inputFileNames,? ? atlasDir=atlasDir,? ? savePath=args.outputDirectory,? ? userModelSpecifications=userModelSpecifications,? ? userOptimizationOptions=userOptimizationOptions,? ? targetIntensity=110,? ? targetSearchStrings=[ 'Cerebral-White-Matter' ],? ? visualizer=visualizer,? ? saveHistory=args.history,? ? saveMesh=args.save_mesh,? ? savePosteriors=savePosteriors,? ? saveWarp=args.save_warp,? ? modeNames=args.mode,? ? pallidumAsWM=(not args.pallidum_separate),? ? saveModelProbabilities=args.save_probabilities,? ? gmmFileName=args.gmm,? ? ignoreUnknownPriors=args.ignore_unknown,) if args.lesion: ? ? # If lesion mask pattern is not specified, assume inputs are T1-contrast? ? lesion_mask_pattern = args.lesion_mask_pattern? ? if lesion_mask_pattern is None:? ? ? ? lesion_mask_pattern = [0] * len(args.inputFileNames)? ? ? ? print('Defaulting lesion mask pattern to %s' % str(lesion_mask_pattern)) ? ? # Delay import until here so that tensorflow doesn't get loaded unless needed? ? from freesurfer.samseg.SamsegLesion import SamsegLesion? ? samseg = SamsegLesion(**samseg_kwargs,? ? ? ? numberOfPseudoSamplesMean=args.lesion_pseudo_samples[0],? ? ? ? numberOfPseudoSamplesVariance=args.lesion_pseudo_samples[1],? ? ? ? rho=args.lesion_rho,? ? ? ? intensityMaskingSearchString=args.lesion_mask_structure,? ? ? ? intensityMaskingPattern=lesion_mask_pattern,? ? ? ? numberOfBurnInSteps=args.burnin,? ? ? ? numberOfSamplingSteps=args.samples,? ? ? ? threshold=args.threshold? ? ) else:? ? samseg = samseg.Samseg(**samseg_kwargs) _, _, _, optimizationSummary = samseg.segment(? ? costfile=costfile,? ? timer=timer,? ? transformFile=args.reg,? ? initTransformFile=args.init_reg,? ? reg_only=args.reg_only) # Save a summary of the optimization processwith open(costfile, 'a') as file:? ? for multiResolutionLevel, item in enumerate(optimizationSummary):? ? ? ? file.write('atlasRegistrationLevel%d %d %f\n' % (multiResolutionLevel, item['numberOfIterations'], item['perVoxelCost'])) timer.mark('run_samseg complete') xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx PS. Repeating the syntax from below. run_samseg --input /home/developer/subjects_new/o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T30-acc_orig__S689126_I1001975.nii /home/developer/subjects_new/rT1_o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T2-FLAIR__S689135_I1001984.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /home/developer/subjects_new/Lesion-test/ -----Original Message----- From: fsbuild <fsbuild(a)contbay.com> To: freesurfer(a)nmr.mgh.harvard.edu Cc: daedalus39(a)aol.com Sent: Thu, Feb 24, 2022 5:15 pm Subject: Re: [Freesurfer] SAMSEG "lesion" (Illegal instruction) ~ running VM_67 Hello Randy, I think the expectation is for users to run ?samseg? from the command line. ?(The samseg script is a front-end you run with command line options, e.g., ?help, which calls samseg_run that in turn runs the samseg python scripts in the freesurfer python distribution which includes the tensorflow code). I can?t speak to the validity of the command + options causing the crash, but I would look too see if a ?core? file was written in the directory where the command ran that produced the ?Illegal instruction? error and subsequent crash. ?The core file might also be under /var/crash. ?If you have the core file you could name it something unique and try uploading it to?https://secure-web.cisco.com/1_8ugcIT497YTUyY1vRRMjZbWfONaiAbR1P1Zg9-6zN… someone to look at. - R. On Feb 24, 2022, at 11:58, daedalus39(a)aol.com wrote: ????????External Email - Use Caution???????? Following up on yesterday's email: I looked up the help text for SAMSEG on the VM (?run_samseg ?help?).??The flag for --lesion indicates that Tensorflow is required.???? --lesion??????? Enable lesion segmentation (requires tensorflow).?I'm not sure is tensorflow is installed in VM_67, but "which tensorflow" returned nothing.? While my question only reported the ?core dump? and a request to check the syntax, I did ask if the ?lesion? flag was implemented in the VM.?? If it's not installed in VM_67, would you be able to offer some guidance as to where the safest download site is and some suggestions as to how to install it? Sincerely, -Randy -----Original Message----- From: daedalus39(a)aol.com To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Sent: Wed, Feb 23, 2022 1:19 pm Subject: SAMSEG "lesion" (Illegal instruction) ~ running VM_67 Dear Experts, I am trying to test SAMSEG "lesion" on VM_67 and after I entered: run_samseg --input /home/developer/subjects_new/o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T30-acc_orig__S689126_I1001975.nii /home/developer/subjects_new/rT1_o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T2-FLAIR__S689135_I1001984.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /home/developer/subjects_new/Lesion-test/ ...I got the following error Illegal instruction (core dumped) Is there anything glaringly wrong in my instruction/input phrase? Is SAMSEG "lesion" implemented in the new VM?? I was able to test the "basic" SAMSEG with a single T1 earlier this morning (it ran just fine) Thanks in advance for any help. -Randy_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1ajCHs20Ntg5vd9AD9I6GP72nyffMyNANWVvUGOngP_c0a…

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Re: [Freesurfer] Annotation File ROIs to Volume
by Jacoby, John 28 Feb '22

28 Feb '22

Ah yep sorry, I see it. Thank you! Best, John

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Fwd: Gcut error: gcutted brain is much smaller than the mask.
by Begüm Cerrahoğlu 28 Feb '22

28 Feb '22

External Email - Use Caution Dear developers, I am trying to clean up the extra dura left after skullstripping. Watershed parameter does not prove to be much helpful and when I try gcut I get the error below. In the archives I came across this exact problem before, https://secure-web.cisco.com/1JREA1RCtgfPRaolYsneD7S5EwcqlaqoCEQHN3rqgzcSwx… However, there was not an end solution available in the archived email exchange. I am not interested in cerebellum and am okay with cutting the cerebellum out of the brain mask as long as it does not interfere with being able to distinctly separate cortex from cerebellum in the following steps. From skullstripping tutorials, I have read that one should not start erasing cerebellum from the brainmask directly and was wondering if you could let me know why? In sum, are there important reasons to keep the cerebellum despite only being interested in analyzing the cortex? If not, could you please let me know what could be the reason for gcut's failure and if there is anyway to disable failure detection so I can see if the gcutted brain is usable? >> " rm -f brainmask.gcuts.mgz >> mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz >> brainmask.gcuts.mgz >> >> INFO: Care must be taken to thoroughly inspect your data >> when using mri_gcut. In particular, inspect the edges of >> gm and cerebellum for over-aggressive cutting. >> Add -segmentation brainmask.gcuts.mgz to the tkmedit >> command string to view the voxels which gcut has removed. >> >> reading mask... >> white mean: 107.529232 >> threshold set to: 107.529232*0.400000=43.011693 >> calculating weights... >> doing mincut... >> now doing maxflow, be patient... >> g-cut done! >> post-processing... >> post-processing done! >> masking... >> ** Gcutted brain is much smaller than the mask! >> ** Using the mask as the output instead! >> >> cp brainmask.auto.mgz brainmask.mgz " 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0. 2) Platform: Linux Mint 20.2 Thank you greatly for your time and efforts. Kindest regards, Begum Cerrahoglu

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How to make a planar cut in Freeview 7.1.1
by Brandon Ingram 27 Feb '22

27 Feb '22

External Email - Use Caution Hi all, I have been trying to create a flat patch of occipital cortex using the following tutorial (https://secure-web.cisco.com/18Kww5tnkyQOlM1ft0T_n7raXdSOUfLM9sJBa4TZ-zMjq2…) I have tried following the instructions in Freeview and am able to create a cut down the calcarine sulcus, but cannot find the “cut plane” button described. I was wondering whether this is implemented in Freeview, or whether this tool is only available in tksurfer? Freesurfer Version: 7.1.1 OS: Mac OS, Monterey 12.2.1 Many thanks! Brandon

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Re: [Freesurfer] SAMSEG "lesion" (Illegal instruction) ~ running VM_67
by fsbuild 26 Feb '22

26 Feb '22

External Email - Use Caution Hello Randy, I think the expectation is for users to run “samseg” from the command line.  (The samseg script is a front-end you run with command line options, e.g., —help, which calls samseg_run that in turn runs the samseg python scripts in the freesurfer python distribution which includes the tensorflow code). I can’t speak to the validity of the command + options causing the crash, but I would look too see if a “core” file was written in the directory where the command ran that produced the “Illegal instruction” error and subsequent crash.  The core file might also be under /var/crash.  If you have the core file you could name it something unique and try uploading it to https://secure-web.cisco.com/13zdjoSMY5sCPpxW673b6aDxUESbBUC7j-BF_P… someone to look at. - R. On Feb 24, 2022, at 11:58, daedalus39(a)aol.com wrote:        External Email - Use Caution        Following up on yesterday's email:I looked up the help text for SAMSEG on the VM (“run_samseg –help”).  The flag for --lesion indicates that Tensorflow is required.     --lesion        Enable lesion segmentation (requires tensorflow). I'm not sure is tensorflow is installed in VM_67, but "which tensorflow" returned nothing.  While my question only reported the “core dump” and a request to check the syntax, I did ask if the “lesion” flag was implemented in the VM.  If it's not installed in VM_67, would you be able to offer some guidance as to where the safest download site is and some suggestions as to how to install it?Sincerely,-Randy-----Original Message-----From: daedalus39(a)aol.comTo: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>Sent: Wed, Feb 23, 2022 1:19 pmSubject: SAMSEG "lesion" (Illegal instruction) ~ running VM_67Dear Experts,I am trying to test SAMSEG "lesion" on VM_67 and after I entered:run_samseg --input /home/developer/subjects_new/o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T30-acc_orig__S689126_I1001975.nii /home/developer/subjects_new/rT1_o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T2-FLAIR__S689135_I1001984.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /home/developer/subjects_new/Lesion-test/...I got the following errorIllegal instruction (core dumped)Is there anything glaringly wrong in my instruction/input phrase?Is SAMSEG "lesion" implemented in the new VM?  I was able to test the "basic" SAMSEG with a single T1 earlier this morning (it ran just fine)Thanks in advance for any help.-Randy_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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