Freesurfer June 2017

freesurfer@nmr.mgh.harvard.edu

116 participants
186 discussions

slips on the 3D surface
by Michael Davies 24 Jun '17

24 Jun '17

Hello, i have noticed a blip or two on a few of my inflated 3D surfaces and have not been able to edit them away as yet. I have made manual adjustments to the pial boundaries, intensity normalization and wm volume in the 2D surface stage but none of these correct the problem after running recon-all. Do you have any suggestions as to how to correct this problem please? [cid:a282ee22-f118-4ca6-8bd8-7f642d8f7ce5] Kind regards, Michael

2 1

How to obtain MNI coordinates
by AKUDJEDU, THEOPHILUS 24 Jun '17

24 Jun '17

Hi All, I am trying to visualise nodes of a brain network reconstructed using FreeSurfer Desikan-Killiany Atlas parcellation scheme (aparc+aseg.mgz) on Brain Net Viewer and Network Based Statistics software. In order to do so, I need to upload a .txt file listing Freesurfer labels coordinates in MNI space. Is there any way I can get a list of MNI coordinates for my set of labels? Many thanks, Theo

1 0

Fw: 答复: When running mkcontrast-sess: A fatal error hasbeen detected by the Java Runtime Environment
by 杨国春 23 Jun '17

23 Jun '17

Does anyone have some idea about this? Are there other ways to analyze functional data on surface? -----原始邮件----- 发件人: "Guochun Yang" <yanggc(a)psych.ac.cn> 发送时间: 2017年6月21日星期三收件人: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> 抄送: 主题: 答复: [Freesurfer] When running mkcontrast-sess: A fatal error hasbeen detected by the Java Runtime Environment Yes the matlab runs well. I remember that I have met some error like “ERROR: cannot find matlab. Is it in your path?” Then I recognize that I always open matlab by typing capital MATLAB rather than lowercase. So I copied /usr/local/MATLAB/R2016b/bin/glnxa64/MATLAB as /usr/local/MATLAB/R2016b/bin/glnxa64/matlab. The above error was fixed but I got the errors in my last email. I don’t know whether the error has something to do with the copyfile. But I cannot delete it, otherwise matlab cannot be found again. 发件人: Douglas Greve 发送时间: 2017年6月20日 11:37 收件人: freesurfer(a)nmr.mgh.harvard.edu 主题: Re: [Freesurfer] When running mkcontrast-sess: A fatal error hasbeen detected by the Java Runtime Environment this appears to be some kind of matlab problem. Can you otherwise run matlab ok? On 6/15/17 5:17 PM, 杨国春 wrote: Hello FreeSurfer Developers, I'm attempting to run 1st-level analysis with FS-FAST, following the tutorial here http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastFirstLevel. I could run mkanalysis-sess successfully: mkanalysis-sess \ -fsd bold -surface fsaverage lh -fwhm 6 \ -event-related -paradigm onset_cond.par -nconditions 5 \ -spmhrf 0 -TR 2 -refeventdur 2 -nskip 0 -polyfit 2 \ -analysis fmcpr.sm6.fsaverage.lh -per-run -force But when I run mkmkcontrast-sess with the following parameters: mkmkcontrast-sess -analysis fmcpr.sm6.fsaverage.lh -contrast vSSI-v-vSSC -a 2 -c 1 it failed and reported error: ------------------------------------------Error------------------------------------------------------------------------ INFO: Found 5 Non-Null Conditions INFO: Found 1 Delays Condition Weights: -1.00000000000000000000 1.00000000000000000000 0 0 0 mkcontrast2 -config fmcpr.sm6.fsaverage.lh/vSSI-v-vSSC.config -anadir fmcpr.sm6.fsaverage.lh -wcond -1.00000000000000000000 1.00000000000000000000 0 0 0 -sumconds -o fmcpr.sm6.fsaverage.lh/vSSI-v-vSSC.mat -wdelay 1 -no-octave $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ cmtxfile fmcpr.sm6.fsaverage.lh/vSSI-v-vSSC.mat nconds 5, wcond -1.00000000000000000000 1.00000000000000000000 0 0 0 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau cmtxfile fmcpr.sm6.fsaverage.lh/vSSI-v-vSSC.mat monly 0 NCond 5 WCond -1.00000000000000000000 1.00000000000000000000 0 0 0 NDelay 1 WDelay 1 TER 0.050000 sumconds 1 sumdelays 0 nircorr 0 TPreStim 0 RmPreStim 0 rdelta 0 0 rtau 0 0 ndelays 1 CNorm 1 setwdelay 0 setwcond 0 Matlab file is /tmp/mkcontrast2.4735.m # # A fatal error has been detected by the Java Runtime Environment: # SIGSEGV (0xb) at pc=0x00007f9d60d795ac, pid =4928, tid=140313822955264 # # JRE version: Java(TM) SE Runtime Environment (7.0_60-b19) (build 1.7.0_60-b19) # Java VM: Java HotSpot(TM) 64-Bit Server VM (24.60-b09 mixed mode linux-amd64 compressed oops) # Problematic frame: # C [libmwuix.so+0x455ac] uixDisplayInformation::getTopWindow() const+0xc # # Core dump written. Default location: /home/amazinger/Public/share/fMRI/CrossModal/Imges/freesurfer/my-functional/core or core.4928 # # If you would like to submit a bug report, please visit: # http://bugreport.sun.com/bugreport/crash.jsp # The crash happened outside the Java Virtual Machine in native code. # See problematic frame for where to report the bug. matlab: javainit.cpp:1389: void {anonymous}::mwJavaAbort(): Assertion `Fatal Java Exception. See Java Crash Report for details.' failed. ------------------------------------------------------------------------ Assertion detected at Thu Jun 15 15:57:34 2017 ------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Crash Mode : continue (default) Current Visual : None Default Encoding : UTF-8 GNU C Library : 2.23 stable Host Name : X1 Java Crash Report : /home/amazinger/hs_error_pid4928.log MATLAB Architecture : glnxa64 MATLAB Root : /usr/local/MATLAB/R2016a MATLAB Version : 9.0.0.341360 (R2016a) Operating System : Linux 4.4.0-79-generic #100-Ubuntu SMP Wed May 17 19:58:14 UTC 2017 x86_64 Processor ID : x86 Family 6 Model 78 Stepping 3, GenuineIntel Virtual Machine : Java 1.7.0_60-b19 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode Window System : No active display Fault Count: 1 Assertion in void {anonymous}::mwJavaAbort() at javainit.cpp line 1389: Fatal Java Exception. See Java Crash Report for details. Register State (captured): RAX = 00007f9d5b92bf60 RBX = 00007f9d751b8878 RCX = 000000000000000a RDX = 00007f9d75198c20 RSP = 00007f9d5b92bd70 RBP = 00007f9d5b92c130 RSI = 00007f9d74f4f3b8 RDI = 00007f9d5b92bd80 R8 = 0000000000000000 R9 = 00007f9d5aa0b8e0 R10 = 00007f9d74dc70b8 R11 = 00007f9d5b92bdf4 R12 = 00007f9d5aa0b1bb R13 = 00007f9d5aa0b8e0 R14 = 00007f9d751a87e8 R15 = 00007f9d5b92c9a0 RIP = 00007f9d74ebc59e EFL = 00007f9d5b92bf88 CS = b94f FS = 7b24 GS = 7f9d Stack Trace (captured): [ 0] 0x00007f9d74ebc59e /usr/local/MATLAB/R2016a/bin/glnxa64/libmwfl.so+01082782 _ZN2fl4diag5linux6x86_6412context_base12capture_dataEv+00000030 [ 1] 0x00007f9d74eb8541 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwfl.so+01066305 [ 2] 0x00007f9d74eb9bd0 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwfl.so+01072080 [ 3] 0x00007f9d74eb9c42 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwfl.so+01072194 [ 4] 0x00007f9d5a9cc75a /usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+01099610 [ 5] 0x00007f9d5960f8bb /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+08513723 [ 6] 0x00007f9d5978fbc7 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+10087367 [ 7] 0x00007f9d596147cf /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+08533967 JVM_handle_linux_signal+00000335 [ 8] 0x00007f9d7919b390 /lib/x86_64-linux-gnu/libpthread.so.0+00070544 [ 9] 0x00007f9d60d795ac /usr/local/MATLAB/R2016a/bin/glnxa64/matlab_startup_plugins/../../../bin/glnxa64/libmwuix.so+00284076 _ZNK21uixDisplayInformation12getTopWindowEv+00000012 [ 10] 0x00007f9d60d66425 /usr/local/MATLAB/R2016a/bin/glnxa64/matlab_startup_plugins/../../../bin/glnxa64/libmwuix.so+00205861 [ 11] 0x00007f9d60d667a5 /usr/local/MATLAB/R2016a/bin/glnxa64/matlab_startup_plugins/../../../bin/glnxa64/libmwuix.so+00206757 [ 12] 0x00007f9d6a34cd71 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwiqm.so+00650609 [ 13] 0x00007f9d6a353d7b /usr/local/MATLAB/R2016a/bin/glnxa64/libmwiqm.so+00679291 [ 14] 0x00007f9d6a39c39e /usr/local/MATLAB/R2016a/bin/glnxa64/libmwiqm.so+00975774 [ 15] 0x00007f9d7a4ae656 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwservices.so+02451030 _Z18svWS_PostUserEventil+00000038 [ 16] 0x00007f9d470c54e7 /usr/local/MATLAB/R2016a/bin/glnxa64/libnativejmi.so+01000679 _ZN5boost6detail8function26void_function_obj_invoker3INS_3_bi6bind_tIvPFvP7JNIEnv_P8_jobjectENS3_5list2INS_3argILi1EEENSC_ILi2EEEEEEEvS6_S8_lE6invokeERNS1_15function_bufferES6_S8_l+00000023 [ 17] 0x00007f9d470d13cc /usr/local/MATLAB/R2016a/bin/glnxa64/libnativejmi.so+01049548 _ZNK5boost9function3IvP7JNIEnv_P8_jobjectlEclES2_S4_l+00000028 [ 18] 0x00007f9d470c456e /usr/local/MATLAB/R2016a/bin/glnxa64/libnativejmi.so+00996718 _Z17PostMatlabMessageP7JNIEnv_P8_jobjectS2_l+00000222 [ 19] 0x00007f9d4e3c9d98 <unknown-module>+00000000 [ 20] 0x00007f9d4e3bd058 <unknown-module>+00000000 [ 21] 0x00007f9d4e3bd058 <unknown-module>+00000000 [ 22] 0x00007f9d4e3bd058 <unknown-module>+00000000 [ 23] 0x00007f9d4e3bd058 <unknown-module>+00000000 [ 24] 0x00007f9d4e3bd233 <unknown-module>+00000000 [ 25] 0x00007f9d4e3bd233 <unknown-module>+00000000 [ 26] 0x00007f9d4e3b74e7 <unknown-module>+00000000 [ 27] 0x00007f9d593f08f5 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06289653 [ 28] 0x00007f9d593ef358 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06284120 [ 29] 0x00007f9d593b37ca /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06039498 [ 30] 0x00007f9d593b3a24 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre /lib/amd64/server/libjvm.so+06040100 [ 31] 0x00007f9d593b3e7a /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06041210 [ 32] 0x00007f9d59535b0e /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+07621390 [ 33] 0x00007f9d59535c76 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+07621750 [ 34] 0x00007f9d593e8d1f /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06257951 [ 35] 0x00007f9d4e3d4e88 <unknown-module>+00000000 [ 36] 0x00007f9d4e3bd058 <unknown-module>+00000000 [ 37] 0x00007f9d4e3b74e7 <unknown-module>+00000000 [ 38] 0x00007f9d593f08f5 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06289653 [ 39] 0x00007f9d593ef358 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06284120 [ 40] 0x00007f9d593b37ca /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06039498 [ 41] 0x00007f9d593b3a24 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06040100 [ 42] 0x00007f9d593b3e7a /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06041210 [ 43] 0x00007f9d59467d26 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06778150 [ 44] 0x00007f9d5947835a /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06845274 JVM_FindClassFromClassLoader+00000490 [ 45] 0x00007f9d515df68c /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/libjava.so+00054924 Java_java_lang_Class_forName0+00000300 [ 46] 0x00007f9d4e3c9d98 <unknown-module>+00000000 [ 47] 0x00007f9d4e3bd233 <unknown-module>+00000000 [ 48] 0x00007f9d4e3bd233 <unknown-module>+00000000 [ 49 ] 0x00007f9d4e3bd058 <unknown-module>+00000000 [ 50] 0x00007f9d4e3b74e7 <unknown-module>+00000000 [ 51] 0x00007f9d593f08f5 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06289653 [ 52] 0x00007f9d593ef358 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06284120 [ 53] 0x00007f9d59429099 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06520985 [ 54] 0x00007f9d59431a1d /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06556189 [ 55] 0x00007f9d5a9d3b91 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+01129361 [ 56] 0x00007f9d5a9cd9f4 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+01104372 [ 57] 0x00007f9d5a9d3174 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+01126772 [ 58] 0x00007f9d5a9d3300 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+01127168 [ 59] 0x00007f9d5a99961b /usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+00890395 [ 60] 0x00007f9d5a996bc5 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+00879557 _ZN3jmi3jmi23JmiMethodsUsedByRuntime4initERKN8services6config14JmiInitOptionsE+00000021 [ 61] 0x00007f9d6a03d5c1 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwmcr.so+00783809 [ 62] 0x00007f9d6a0380ab /usr/local/MATLAB/R2016a/bin/glnxa64/libmwmcr.so+00762027 [ 63] 0x00007f9d6a028196 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwmcr.so+00696726 [ 64] 0x00007f9d6a014cfd /usr/local/MATLAB/R2016a/bin/glnxa64/libmwmcr.so+00617725 [ 65] 0x00007f9d791916ba /lib/x86_64-linux-gnu/libpthread.so.0+00030394 [ 66] 0x00007f9d78ec782d /lib/x86_64-linux-gnu/libc.so.6+01075245 clone+00000109 [ 67] 0x0000000000000000 <unknown-module>+00000000 If this problem is reproducible, please submit a Service Request via: http://www.mathworks.com/support/contact_us/ A technical suppo rt engineer might contact you with further information. Thank you for your help.** This crash report has been saved to disk as /home/amazinger/matlab_crash_dump.4928-1 ** MATLAB is exiting because of fatal error Killed -----------------------------------------END------------------------------------------------------------------------- It also created an error log and a matlab crash file, which I attached to this email. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all. log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu Kylin 16.04 LTS 3) uname -a: Linux X1 4.4.0-79-generic #100-Ubuntu SMP Wed May 17 19:58:14 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log and error logs: see attached Best Regards Guochun Yang Institute of Psychology, Chinese Academy of Sciences _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 祝好！ Best Regards 杨国春（刘勋组） Guochun Yang 中科院心理所 Institute of Psychology, Chinese Academy of Sciences

1 0

results not displayed graphically in Qdec
by francesca ponteduro 23 Jun '17

23 Jun '17

Dear Experts, I am sorry to re-send this email for the third time, but I haven't received any answer because probably you haven't seen it, as you are really busy. I am having some trouble with the display of the area in Freesurfer/Qdec. In particular, after running the analysis, I can see some results in the terminal but in the display section of Qdec, no areas are shown . I have tried to wait or re-launch the analysis but the result was the same. What shall I do in order to have the result displayed properly? thank you again for your time, BW Francesca

1 0

tksurfer- configure overlay display
by Ladan Shahshahani 23 Jun '17

23 Jun '17

Hi, I'm trying to show an overlay (.mgh file) I have created. I'm using tksurfer to view the file. I intend to change the color scale using view/configure/overlay. However, the *configure overlay display* window is clipped and I can not see the apply button. *Tksurferguide* says that it may happen using low-resolution monitors and says that I need to download and copy a file into $FREESURFER_HOME/lib/tcl directory ( https://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferWorkingWith…) Trying to download this file, I get the following message: *Alert550 Failed to change directory* How can I solve this problem? Can someone send me the file? Bests, Ladan

1 0

WM edits
by Manuel Delgado 23 Jun '17

23 Jun '17

Regarding this issue: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53772.html and a question I previously raised: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52168.html I still have some concerns I would like to share. 1) Is it necessary to fill in parts of the ventricles that have not been included in yellow in the wm mask? 2) How to proceed with those little holes which do not affect the wm surface (image 1)? 3) Conversely, how to deal with little "spots" of wm mask which are frequently found in medial temporal areas (such as those in the enclosed image 2)? and 4) what surface must we take as a reference to make oll the edits, the wm or the smoothwm.nofix? Thanks for your patience. Best -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN

1 0

Saving isosurfaces based on Index
by skhu770＠aucklanduni.ac.nz 22 Jun '17

22 Jun '17

Hi there, I want to save each individual isosurface, from the aparc.a2009s+aseg.mgz segmentation, as its own .vtk file based on Index number. Is this possible? If so, which commands can be used?

1 0

FreeSurfer Boston Course Registration now open!
by Allison Stevens 22 Jun '17

22 Jun '17

The FreeSurfer group is offering a four-day FreeSurfer Tutorial and Workshop, September 25th to September 28th, 2017 at the Martinos Center for Biomedical Imaging in Charlestown, MA. You can find the link to the registration page at the top of our course website: https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription Details about the content of the course, the location, registration fees, accepted payment types, and nearby hotels is currently on the website above. Please read the above page in its entirety before registering and before sending questions. At the course, laptops are provided with FreeSurfer and practice data already installed. Attendees will work in pairs (sharing a laptop). If you are not one of the first 50 to register, you will be put on a waiting list and will be notified if a spot becomes available. We have enrolled people into the course from the waiting list every time we held a course so don't be dismayed if you end up on the waiting list. Allison Stevens Lab Manager/Course Organizer FreeSurfer Development Team Laboratory for Computational Neuroimaging Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging

1 0

Segmentation problem recon-all
by Lisa Delalande 22 Jun '17

22 Jun '17

Hi, I am a PhD student and faced a problem with Freesurfer, more specially with segmentation. First of all, I did a typical qsub command. However, when I cheked with tkmedit, I saw problems of brainsmask. Indeed, meninges are often considered as grey matter. I tried these different commands : 1.) setenv SUBJECTS_DIR /path/to/your/data setenv WATERSHED_PREFLOOD_HEIGHTS '20 30 40 50' recon-all -multistrip -clean-bm -s <subjid> -no-isrunning 2.) recon-all -skullstrip -clean-bm -gcut -subjid <subjid> cd $SUBJECTS_DIR/yoursubj/mri/transforms cp talairach_with_skull.lta bak cp talairach_with_skull_2.lta talairach_with_skull.lta recon-all -s yoursubj -skullstrip -clean-bm -clean-lta" without success I finally used a manual method : 3.) tkmedit skullstrip3_before brainmask.mgz -aux T1.mgz but the latter is source of error and time-consuming. I've got 105 MRI scans to rectify. Do you have a council to improve le first step of the reconn-all ? Sincerely Marine Moyon

2 3

error report - talairach.m3z not found
by Ramesh Babu 22 Jun '17

22 Jun '17

Dear Expert, The recon-all -all process has stopped abruptly and error report shows that "cannot find or read transforms/talairach.m3z". Please see the attached file. Processing was running in 5 terminal simultaneously and it has happened for two processing. Others exited without error. Could please tell what should I do to continue the interrupted one. Thanks in advance Ramesh

3 5

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Freesurfer June 2017