Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

Skull striping problems
by MATEUS ROZALEM ARANHA 25 Aug '17

25 Aug '17

Hi! When I run recon-all on my data, some skull and dura is left behind and affects the surfaces and the parcellation. I re-run the data using a lower watershed (I tried 20, 15, 10 and 05). The brainmask changed, but the remaining skull still affects the parcellation and surfaces. My doubt is: when I re-run my data using a lower watershed value, does it automatically create new surfaces and volumes or not? If not, how can I reset it? Best Mateus

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Re: [Freesurfer] recon-all error
by Cara Bohon 24 Aug '17

24 Aug '17

This is the first time I have had the message that it exited with errors. The first times I ran it, it just stopped and the log file ended without a summary statement of why the job stopped. I assumed that time was because I was running it on a cluster with a 24 hour time limit, so I extended the job to 48 hours and started the job again - this time I got the error described below. How long is reasonable to be stuck on fix topology for one hemisphere? I guess my fear was that if it hadn't finished in 48 hours, there was something wrong. > does this happen every time you run it? The message said that the job > was killed, which suggests something outside of recon-all (eg, if you > were running it on a cluster, sometimes a job will get killed if it runs > out of memory or runs too long). > > > On 08/23/2017 02:30 PM, Cara Bohon wrote: >> I have a couple of subjects "exited with ERRORS" after running almost 48 hours (when my others all took about 13-15 hours on the same server). Both exited during Fix Topology lh. >> >> The only time "error" appears is in this line: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 - which prior messages to this list suggest is not meaningful or problematic. >> >> I am brand new to Freesurfer, so I'm not quite sure where to start in troubleshooting. The orig.mgz file looks fine to me, but maybe I'm missing something. Any other tips for things to check? I'm attaching a recon-all.log file in case that is helpful. I am running Freesurfer 5.3.0 on Linux. >> >> Thanks for any tips on addressing the error! >> >> -Cara

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Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding
by Fred Lado 24 Aug '17

24 Aug '17

Dear FS gurus, I just want to give some feedback on an error message that has bedeviled some of us for the last few months even after running fs_update and turning off SIP. I have been getting this error when I ran mri_coreg or mris_convert: dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib In my case there were multiple versions of libgomp.1.dylib. One in the current Freesurfer 6.0 install, one in the gcc-7.1 compiler library that I recently installed (after I ran into this error) and the third from an ANFI install from 2013. When I rearranged the order of the PATH as shown, the error went away. This was my old path: /usr/local/bioimagesuite35:/usr/local/bioimagesuite35/sbin:/usr/local/bioimagesuite35/bin:/usr/local/bioimagesuite35/bin:/Users/fred/Dropbox/Research_Scripts/EpiSurg-iElvis/iELVis/iELVis_BASH:/Users/fred/Dropbox/Research_Scripts/Linux-Scripts:/Applications/MATLAB_R2015a.app/bin/:/usr/local/cuda/bin:/usr/local/AFNI:/usr/local/fsl/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/git/bin:/usr/local/fsl/bin:/usr/local/afni This is my new path: /Users/fred/Dropbox/Research_Scripts/EpiSurg-iElvis/iELVis/iELVis_BASH:/Users/fred/Dropbox/Research_Scripts/Linux-Scripts:/usr/local/gcc-7.1/bin:/Applications/MATLAB_R2015a.app/bin/:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/fsl/bin:/usr/local/AFNI:/usr/local/bioimagesuite35:/usr/local/bioimagesuite35/sbin:/usr/local/bioimagesuite35/bin:/usr/local/bioimagesuite35/bin:/usr/local/cuda/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/git/bin:/usr/local/fsl/bin:/usr/local/afni Best, Fred Fred Lado, MD PhD Director, Epilepsy - Central and Eastern Regions Northwell Health 917-608-1881 (mobile) 516-325-7000 (practice) 516-325-7001 (fax) flado(a)northwell.edu Confidentiality Notice: This document is protected by EDUCATIONAL LAW 6527 PUBLIC HEALTH LAW 2085, J, K, L, M. This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited and may be unlawful. If you are not the intended recipient, please delete this e-mail immediately. > On Aug 24, 2017, at 12:00 PM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > 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: recon-all error (Douglas N Greve) > 2. Re: Continuous co-variate by continuous co-variate > interaction effects (Douglas N Greve) > 3. Re: Hard failure via XNAT pipeline (Freesurfer 6) > (Rockers, Elijah D.) > 4. Using Total Cortical White Matter Volume as a "whole brain" > covariate (Mehta, Chintan) > 5. Re: mri_coreg (Douglas N Greve) > 6. Functional Connectivity Motion Regression (Leathem, Logan Daniel) > 7. Qdec keyboard input error (???) > 8. Xlib: extension "GLX" missing on display "0.0" when running > freeview (fengmei fan) > 9. cudadetect fails: wrong amount of memory and number of cores > detected (Markus.Mertens(a)evkb.de) > 10. Re: mri_coreg (Joudy.carter) > 11. Re: QA tools for FS vs 6.0 (Antonietta Pepe) > 12. sub cortical analysis (John Anderson) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 23 Aug 2017 14:54:29 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] recon-all error > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <b83cfed1-8a92-fcc7-8ce5-96ec093e10fc(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > does this happen every time you run it? The message said that the job > was killed, which suggests something outside of recon-all (eg, if you > were running it on a cluster, sometimes a job will get killed if it runs > out of memory or runs too long). > > > On 08/23/2017 02:30 PM, Cara Bohon wrote: >> I have a couple of subjects "exited with ERRORS" after running almost 48 hours (when my others all took about 13-15 hours on the same server). Both exited during Fix Topology lh. >> >> The only time "error" appears is in this line: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 - which prior messages to this list suggest is not meaningful or problematic. >> >> I am brand new to Freesurfer, so I'm not quite sure where to start in troubleshooting. The orig.mgz file looks fine to me, but maybe I'm missing something. Any other tips for things to check? I'm attaching a recon-all.log file in case that is helpful. I am running Freesurfer 5.3.0 on Linux. >> >> Thanks for any tips on addressing the error! >> >> -Cara >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 2 > Date: Wed, 23 Aug 2017 14:57:53 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Continuous co-variate by continuous > co-variate interaction effects > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <e1a5bf46-9c3f-564b-fbe0-ce081f513ae8(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > Is that your design matrix or the contrast matrix? To test for the > interaction between two continuous variables, one usually creates a new > variable by multiplying them together and then just testing for the > regressor for that variable being different than zero > > > On 08/23/2017 12:34 PM, Timothy Hendrickson wrote: >> Freesurfer experts, >> >> I have created a design matrix in order to test for whether there is >> an interaction effect between two continuous co-variates controlling >> for a categorical variable. >> >> So I have one categorical variable with two levels, and two continuous >> co-variates. >> >> My design matrix is as follows: >> >> 0 0 1 1 0 0 >> 0 0 0 0 1 1 >> >> Is this correct? >> >> -Tim >> >> Timothy Hendrickson >> Department of Psychiatry >> University of Minnesota >> Bioinformatics and Computational Biology M.S. Candidate >> Office: 612-624-6441 >> Mobile: 507-259-3434 (texts okay) >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 3 > Date: Wed, 23 Aug 2017 21:54:20 +0000 > From: "Rockers, Elijah D." <edrockers(a)houstonmethodist.org> > Subject: Re: [Freesurfer] Hard failure via XNAT pipeline (Freesurfer > 6) > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <1503525260.5299.80.camel(a)houstonmethodist.org> > Content-Type: text/plain; charset="utf-8" > > We'll try to process it on a blade server tongiht... if it succeeds we can edit any incorrect results as needed. > > The image is from a separate site, it has OK resolution (1x1x1.5) but has an enormous amount of gibbs ringing compared to our on-site images, which is probably causing the issue... > > Thanks, > Eli > > > > Date: Wed, 23 Aug 2017 11:54:06 -0400 > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] Hard failure via XNAT pipeline (Freesurfer > 6) > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: <54B7B7A7-CDC3-46F1-8E1B-098142FD3DB2(a)nmr.mgh.harvard.edu<mailto:54B7B7A7-CDC3-46F1-8E1B-098142FD3DB2@nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset="us-ascii" > > That defect is so big you probably ran out of memory. > >> On Aug 23, 2017, at 11:21 AM, Rockers, Elijah D. <edrockers(a)houstonmethodist.org<mailto:edrockers@houstonmethodist.org>> wrote: >> >> We encountered a hard failure, below is the tail of the log. We are currently running Freesurfer 6 again locally to see if it succeeds on a desktop machine (this is the first time encountering a hard failure on the XNAT server). Any suggestions? >> >> -merging segment 180 into 178 >> 160 defects to be corrected >> 0 vertices coincident >> reading input surface /data/build/nnac/20170818_114535/alamode_MRI08162017/20170818114538/alamode_MRI08162017/surf/lh.qsphere.nofix... >> reading brain volume from brain... >> reading wm segmentation from wm... >> Computing Initial Surface Statistics >> -face loglikelihood: -8.7982 (-4.3991) >> -vertex loglikelihood: -6.2982 (-3.1491) >> -normal dot loglikelihood: -3.5611 (-3.5611) >> -quad curv loglikelihood: -6.1931 (-3.0965) >> Total Loglikelihood : -24.8505 >> >> CORRECTING DEFECT 0 (vertices=40706, convex hull=11265, v0=89) >> XL defect detected... >> Segmentation fault (core dumped) >> Linux hhvrixnatp01 2.6.32-431.el6.x86_64 #1 SMP Sun Nov 10 22:19:54 EST 2013 x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s alamode_MRI08162017 exited with ERRORS at Mon Aug 21 19:27:09 CDT 2017 >> >> To report a problem, see https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.… >> >> Houston Methodist. Leading Medicine. >> >> Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHo… and https://urldefense.proofpoint.com/v2/url?u=http-3A__facebook.com_HoustonMet… . >> >> ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… >

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Cortical thickness map for a pediatric case
by Sneha Pandya 24 Aug '17

24 Aug '17

Dear team, I have completed cross-sectional pipeline on my pediatric case with a baseline and 4 follow up time points between 4-7 years of age. However, I was not able to run longitudinal pipeline on it as the base template creation failed with some topological errors. I assume this failure is due to large eTIV changes within 4-7 years of age. I wanted to compare cortical thickness map of follow-up time points to its baseline using qdec. However, I was not able to as running qdec with single subject failed with 0 dof error. Can you'll please suggest how can I generate cortical thickness map between follow-up and baseline scans for this subject if qdec is not an option. Thanks, Sneha

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Discrepancy between estimated area of a label
by Sheraz Khan, PhD 24 Aug '17

24 Aug '17

Hi, I am trying to estimate, area of a label on the white surface. I calculated area by summing areas of all the triangles in the label (half of the magnitude of the cross product of the vectors spanning sides of a triangle), when I compared my result with "mris_anatomical_stats" there is a discrepancy, my code underestimate the area. I am wondering is there any correction factor, I am missing ? The gist of the code is at https://gist.github.com/SherazKhan/9cbb5520d4efb39bc90f5b175a60a3c5 Thanks __sk__

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sub cortical analysis
by John Anderson 24 Aug '17

24 Aug '17

Hi Dr Greve, I am using pet surfer to analyze suv images. I followed all the steps in wiki, I used the option mgx then I fed the images mgx.{ctxgm,subctxgm,gm} into surface based analysis for left and right hemispheres. I want to inquire about the sub cortical analysis. 1. I assume the analysis for sub cortical gray matter (i.e. using the images subctxgm) is volumetric. Correct? 2. Are the following steps correct for sub cortical gray matter analysis mri_vol2vol --mov subctxgm.nii.gz --reg reg.dat --tal --talres 2 --talxfm talairach.xfm --nearest --no-save-reg --o subctxgm.tal2mm.nii.gz mri_mask subctxgm.tal2mm.nii.gz $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz subctxgm.tal2mm_subc.nii.gz & Concatenate all subjects together using mri_concat smooth using mri_fwhm (what is the recommended smoothing for suv)? Then Group analysis: mri_glmfit --y all.suvr.tal2mm.subc.sm10.nii --fsgd fsgd.dat --C contrast.mtx --glmdir dir mri_glmfit-sim --glmdir dir --grf 1.3 pos --cwpvalthresh 0.0166 for "mri_glmfit-sim" in subcortical structure is the flag grf correct or cache? Thanks in advance! John

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QA tools for FS vs 6.0
by Antonietta Pepe 24 Aug '17

24 Aug '17

Dear FreeSurfer list, is any of you aware of a new version of the QA (quality assessment) tools < [ https://surfer.nmr.mgh.harvard.edu/fswiki/QATools | https://surfer.nmr.mgh.harvard.edu/fswiki/QATools ] > working for FS vs 6.0? Should I expect a new release in the near feature? Kind regards, Antonietta ANTONIETTA PEPE IMN, Institut des Maladies Neurodégénératives, UMR 5293 Equipe 5 : GIN, Groupe d’Imagerie Neurofonctionnelle, CEA - CNRS - Université de Bordeaux Université de Bordeaux 146 rue Léo Saignat - CS 61292 - Case 28 33 076 Bordeaux cedex [ http://www.imn-bordeaux.org/ | http://www.imn-bordeaux.org/ ]

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mri_coreg
by John Anderson 24 Aug '17

24 Aug '17

Dear Dr Greve, Kindly, I wanted to know why "mri_coreg" apples smoothing during registration. e.g. mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta Are there any effects on the accuracy of smoothing if I turn off this default feature (specifically in pet surfer pipeline). mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta --no-smooth Thank you for any clarification John

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Xlib: extension "GLX" missing on display "0.0" when running freeview
by fengmei fan 24 Aug '17

24 Aug '17

HI, I installed Freesurfer 6 in CentOS 6.5, when runing freeview, errors occurred: Xlib: extension "GLX" missing on display "0.0" Xlib: extension "GLX" missing on display "0.0" What's wrong? And how to settle this problem? Best, Fengmei Fan Assistant professor, Beijing Huilongguan Hospital, Beijing Huilongguan Medical College of Peking University

1 0

Qdec keyboard input error
by 김현우 24 Aug '17

24 Aug '17

I'm studying freesurfer especially, QDEC to execute group analysis. In QDEC, I can type in Subjects and Design tap. But I can't type in Display tap like threshold p. I've seen several question like me but no one give solution. Here's my environment. OS : CentOS 7.0 Freesurfer : stable 6.0 QDEC : 1.5 Show me how to solve this problem. Thank you. ============================================= Hyunwoo Kim Graduate school of Yonsei University Biosignal Processing Laboratory #201 Sanhakgwan, 1 Yonseidaegil, Heungup, Wonju, Gangwon, 220-710, Republic of Korea Tel. +82-33-760-2809

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