Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30068 discussions

pial surface jacobian
by Aniqa DaAsliLovr 20 Jun '17

20 Jun '17

Hi All, I have two questions. 1) Is there a way to calculate a pial surface jacobian ? How do I get this measure ? 2) Is the lh.jacobian_white rh.jacobian_white the deformation to fsaverage or something else ? Please let me know. Thanks Ani

2 1

Regenerating the WM Volume surface
by Michael Davies 20 Jun '17

20 Jun '17

Hello, i am currently having problems with the code required to regenerate the surface when editing the WM Volume. I was wondering if you could provide any tips or advice as to where i am going wrong please? Kind regards, Michael bash-4.1$ freesurfer_setup_freeview -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer_v6.0.0 FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects MNI_DIR /usr/local/freesurfer_v6.0.0/mni FSL_DIR /usr/local/fsl bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj2/Subj2 bash-4.1$ recon-all -autorecon2-wm -autorecon3 -Subj2 ERROR: Flag -Subj2 unrecognized. -autorecon2-wm -autorecon3 -Subj2 Linux pbic.bham.ac.uk 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Tue Jun 20 19:58:38 BST 2017 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

2 2

DODS and DOSS
by marco mcsweeney 20 Jun '17

20 Jun '17

Dear Freesurfer experts, I have a quick question regarding the appropriate design (DOSS or DODS) to be used with QDEC when comparing 2 groups for cortical thickness and LGI values. So far I have used DODS first to look for an age-cortical thickness interaction in both groups. I used the real ages and also demeaned the age variable in my analysis. I entered age as a covariate and as a nuisance factor also. I have gender and diagnosis as discrete and eTIV as nuisance in both analysis. Neither was significant. After this I used DOSS in QDEC to compare groups groups for both cortical thickness and LGI. My questions relates to the use of age as a covariate in DOSS. Is it appropriate to enter age as covariate in DOSS given that DOSS assumes that both groups have the same slope? I have looked through the archives and online for an answer to this but I am still a bit confused. Any help or advice on this would be greatly appreciated. Thank you so much in advance. Best wishes Marco

2 11

fixing messy surfaces
by Meaghan Perdue 20 Jun '17

20 Jun '17

Hello, I am working through manual edits and I've come across a subject with an area of very messy surfaces (both white and pial) despite that the WM mask seems to have been drawn just fine. Please see attached image. This subject was run with the following expert opts since some gray and white matter had been excluded from the surfaces in the initial recon-all. mri_segment -wlo 65 mris_make_surfaces -max_gray_at_csf_border 40 -max_csf 15 -wlo 65 Is there a way to fix these surfaces? Thank you, Meaghan Perdue

1 0

When running mkcontrast-sess: A fatal error has been detected by the Java Runtime Environment
by 杨国春 20 Jun '17

20 Jun '17

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 support 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

4 3

Freesurfer Template Creation
by Daniele Orlandi 20 Jun '17

20 Jun '17

Dear experts, I'm running the Fresurfer Longitudinal Stream and I didn't realize that creating the Template file, some time points were not in the right order: recon-all -base <templateid> -tp <tp3id> -tp <tp1id> -tp <tp4id> -tp <tp2id> -all instead of: recon-all -base <templateid> -tp <tp1id> -tp <tp2id> -tp <tp3id> -tp <tp4id> -all Does it affect the creation of the Template? Thank you again! Best Daniele _____________________________________________________________ Daniele Orlandi, PsyD Laboratory of Alzheimer's Neuroimaging and Epidemiology IRCCS Fatebenefratelli,Via Pilastroni 4,25125 Brescia - Italy T: +39 030 35 01 563 - M: +39 346 50 90 531 daniele.orlandi.psy(a)gmail.com Skype: daniele.orlandi.skype ----- Original Message ----- From: freesurfer-request(a)nmr.mgh.harvard.edu To: freesurfer(a)nmr.mgh.harvard.edu Sent: Thursday, June 15, 2017 11:33:01 PM Subject: Freesurfer Digest, Vol 160, Issue 27 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: viewing 3D surfaces (Michael Davies) 2. Freesurfer parcelations of cortical regions in TrackVis (Leyton Moscoso, Cristian Eduardo) 3. Re: viewing 3D surfaces (Bruce Fischl) 4. Re: mris_anatomical_stats and cortical thickness {Disarmed} {Disarmed} (Hilton, Benjamin Taylor) 5. bvals and bvecs for tracula v6 (Marissa Pifer) 6. Re: bvals and bvecs for tracula v6 (Yendiki, Anastasia) 7. Re: viewing 3D surfaces (Michael Davies) 8. Re: viewing 3D surfaces (Bruce Fischl) 9. substract images (John Anderson) 10. Re: substract images (Bruce Fischl) 11. Re: substract images (John Anderson) 12. Re: viewing 3D surfaces (Michael Davies) 13. Re: substract images (Bruce Fischl) 14. Re: viewing 3D surfaces (Bruce Fischl) 15. Re: Freesurfer parcelations of cortical regions in TrackVis (Lilla Zollei) 16. Re: substract images (John Anderson) 17. Re: substract images (Bruce Fischl) 18. Re: substract images (John Anderson) 19. Cropping of slices during recon-all (Jerry Jeyachandra) 20. When running mkcontrast-sess: A fatal error has been detected by the Java Runtime Environment (???) ---------------------------------------------------------------------- Message: 1 Date: Thu, 15 Jun 2017 16:01:58 +0000 From: Michael Davies <Michael.Davies30(a)hotmail.com> Subject: Re: [Freesurfer] viewing 3D surfaces To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <MM1P123MB1372C65604FABCBCFC7372DF89C00(a)MM1P123MB1372.GBRP123.PROD.OUTLOOK.COM> Content-Type: text/plain; charset="windows-1252" That did it :) thank you so much for your help!! Kind regards, Michael ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu> Sent: 15 June 2017 15:48:31 To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] viewing 3D surfaces Remove the '/' in front of "surf". On 06/15/2017 11:45 AM, Michael Davies wrote: Hi Bruce, i'm getting closer to opening it now. But the final command /surf/lh.pial \ didnt work this time. Any further suggestions? Kind regards, Michael bash-4.1$ freesurfer_setup_freeview -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer_v6.0.0 FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects MNI_DIR /usr/local/freesurfer_v6.0.0/mni FSL_DIR /usr/local/fsl bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage bash-4.1$ freeview -f \ > /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ > /surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \ > /surf/lh.inflated:visible=0 \ > /surf/lh.white:visible=0 \ > /surf/lh.pial \ > --viewport 3d MRISread(/surf/lh.pial): could not open file No such file or directory MRISread failed No such file or directory ould not open file bash-4.1$ ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl(a)nmr.mgh.harvard.edu><mailto:fischl@nmr.mgh.harvard.edu> Sent: 15 June 2017 15:19:21 To: Freesurfer support list Subject: Re: [Freesurfer] viewing 3D surfaces you are not calling freeview in this command. Try putting freeview at the start On Thu, 15 Jun 2017, Michael Davies wrote: > > Hi Bruce, i am still getting error messages. is there anything else i could > try doing? > > Kind regards, Michael > > > bash-4.1$ freesurfer_setup_freeview > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer_v6.0.0 > FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects > MNI_DIR /usr/local/freesurfer_v6.0.0/mni > FSL_DIR /usr/local/fsl > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage > bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ > >/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflat > ed_thickness:visible=0 \ > > /surf/lh.inflated:visible=0 \ > > /surf/lh.white:visible=0 \ > > /surf/lh.pial \ > > --viewport 3d > bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such > file or directory > bash-4.1$ > > > > ____________________________________________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> > <freesurfer-bounces(a)nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu><mailto:fischl@nmr.mgh.harvard.edu> > Sent: 15 June 2017 14:11 > To: Freesurfer support list > Subject: Re: [Freesurfer] viewing 3D surfaces > Hi Michael > > you need to have FreeSurfer in your path or nothing will work. Have you > sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the > environment? > > cheers > Bruce > > > On Thu, 15 Jun 2017, Michael Davies wrote: > > > Hello, i am having problems accessing the 3D surfaces of my data. Is there > > any advice you could provide for me please? > > bash-4.1$ freeview -f \ > >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=apa > r > > c.annot:name=pial_aparc:visible=0 \ > >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overl > a > > y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 > \ > >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visib > l > > e=0 \ > >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible= > 0 > > \ > > > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \ > > > --viewport 3d > > bash: freeview: command not found > > > > Kind regards, Michael > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > Freesurfer Info Page - Harvard University > mail.nmr.mgh.harvard.edu > To see the collection of prior postings to the list, visit the Freesurfer > Archives. A searchable archive which of messages PRIOR to March 2004 is at > ... > > > > The 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 Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

4 4

No keyboard input accepted in freeview and tkmedit
by Caspar M. Schwiedrzik 20 Jun '17

20 Jun '17

Hi! I have a weird issue where tkmedit and freeview both do not accept any keyboard input. This is Freesurfer v5.3 running on Centos 7, connecting via RDP. I saw a couple of posts by other users having this problem, but I could not find any solutions/replies on the mailing list. Does anyone know how to fix this? Thanks, Caspar

2 3

seed to seed replica of fsfast
by Lee, Erik Gordon 20 Jun '17

20 Jun '17

Hi All, I am trying to do some seed to seed functional connectivity calculations that replicate my analysis design in fsfast. I know FreeSurfer 6 has the fcseedcor function, but it appears that this requires a low pass filter, which is not a part of our processing stream. Also I don't think the fcseedcor function has any detrending which is a part of our analysis. I am putting together a Matlab script to do this for me, and want to be sure that the steps are equivalent. This is my normal mkanalysis-sess command: mkanalysis-sess -analysis targ.2cm.rh -surface fsaverage rh -fwhm 6 -notask -taskreg target_2cm.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -fsd rest -TR 3 -per-run -hpf .01 -tpexclude tpe_file -nuisreg global.waveform.dat 1 This is what I am doing in Matlab: -First, I apply a polynomial detrending to all the seeds and nuisance regressors (first five components from vcsf and wm, first three from mcextreg, and one component of global signal), while ignoring any bad timepoints. -Second, I make all signals evenly sampled again by applying a linear interpolation over missing timepoints for both the seeds and nuisance regressors. -Third, I apply a high order high pass filter. -Fourth, I get rid of all the timepoints that were generated from the linear interpolation (now post filtering). -Fifth, I use a glm to regress all the nuisance variables from the ROI signals. -Sixth compute the correlation coefficients between seeds using the residuals from the previous step. How similar is that to what is done in fsfast? Any tips on what to change? Thanks! Erik

2 1

Cropping of slices during recon-all
by Jerry Jeyachandra 20 Jun '17

20 Jun '17

Hi Freesurfer team, I have a compressed nifti file converted from DICOM that I am running through recon-all. From my understanding first mri_convert is run on the original nifti file in order to generate 001.mgz which is then averaged across multiple runs to make rawavg.mgz. Since I'm only using 1 run, rawavg.mgz should be equivalent to 001.mgz. Now I've noticed that compared to simply loading in the original NIFTI image, loading in rawavg.mgz produces a cropped version of the image where the bottom section (neck region and below) is cropped out. In addition the SI axis which used to be 255 voxels in height, is now shorter (different across individuals run through recon-all). With a set of voxel indices in the original NIFTI image, I'd like to find a corresponding set of voxel indices in the cropped rawavg.mgz. Does FreeSurfer store any information related to the cropping that is done, I expect that there is only a translational shift in the SI axis but I'd like to automatically extract this value for each individual I've run through recon-all. Thanks, Jerrold Jeyachandra

2 1

volume, thickness and surface area analyses
by Lim, Lena 20 Jun '17

20 Jun '17

Dear Freesurfer Experts, A review questioned the validity of examining volume in addition to cortical thickness and surface area within the same study. In particular, he commented that "The volume is the product of the thickness and area ...As the product of two Gaussian-distributed variables is not Gaussian-distributed, the volume is likely to violate assumptions of the statistical methods." Could you please kindly advice on this? Many thanks, Lena

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