Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30067 discussions

ROI analyses using SPM AAL ROIs
by M Janani 28 Jun '17

28 Jun '17

Hi Team, Currently I'm working on ROI analyses. I saw one article related to VolumeROICorticalThickness in Free surfer wiki. Could anyone please tell me what is the anatomical file(TT_avg152T1.nii) they are referring to? I took AAL ROIs from SPM. In that case, which anatomical file should I use for my analyses? Any help would be really grateful. Thanks in advance. Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------

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freesufer 6.0 error
by Jinsong Tang 27 Jun '17

27 Jun '17

Dear FreeSurfer experts, When I run the FreeSurfer 6.0. the recon-all exited with ERRORS. Attached is the log file. Can you please let me know how fix this error? Thanks, Jinsong

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mghRead error (ribbon.mg: could not open file)
by Shuo Zhou 27 Jun '17

27 Jun '17

Hello FreeSurfer Developers, I am using recon-all to process the structural mri data. The autorecon1 works fine, however I got the following error when I run the recon-all autorecon2 command: mghRead(/home/acp16sz/openfmri/data/subdir/ds003_sub001/mri/ribbon.mgz, -1): could not open file. I have checked the output of the recon-all steps (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) the file ribbon.mgz is the output of autorecon3, why it is required in autorecon2. Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: 64-bit Scientific Linux (which is Redhat based) HPC 3) uname -a: Linux iceberg-login2 2.6.32-696.3.2.el6.x86_64 #1 SMP Mon Jun 19 11:23:31 CDT 2017 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Kind regards, Shuo Sent from Mail for Windows 10

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cannot open registration file in DTI
by Yifan Xu 27 Jun '17

27 Jun '17

Hi, freesurfer team. when I check my DTI registration and run the below command: the bash terminal always tell me freeview -v $SUBJECTS_DIR/$subj/mri/orig.mgz \ lowb.nii:reg=register.dat \ -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green \ $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green \ -viewport coronal

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Can new-released FS(stable v6.0.0) build in CentOS 6 x86_64 (64b) run on Ubuntu 16.04?
by zonglei.fsl Zhen 26 Jun '17

26 Jun '17

I mean the pre-complied package freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz. Thanks Zonglei

2 1

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

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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

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