Freesurfer June 2016

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smoothing T1 images
by John Anderson 21 Jun '16

21 Jun '16

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Error loading a constructed annotation file
by Bittner, Nora 21 Jun '16

21 Jun '16

Dear freesurfer experts, I constructed an annotation file using mris_label2annot. I did this several times and every time it worked very well. I was able to use a ctab to define several colors, load my annotation file into freeview, and look at it. Now I tried to construct another annotation file in the same manner, but if I try to load it into freeview, freeview just crashes. When I constructed the annotation file I received no error from the terminal output. I can´t understand the error message the terminal gives in the moment freeview crashes. Since I was always successful in constructing my annotation files, I wonder why this happens now. I hope you can tell me, what the attached error message means. Thanking you in advance, Nora Bittner Arbeitsgruppe Konnektivität Institut für Neurowissenschaften und Medizin (INM-1) Forschungszentrum Jülich GmbH 52425 Jülich Tel.: 02461-612412 Email: n.bittner(a)fz-juelich.de<mailto:n.bittner@fz-juelich.de> und Arbeitsgruppe Konnektivität im menschlichen Gehirn C. und O. Vogt Institut für Hirnforschung Heinrich-Heine-Universität Düsseldorf Universitätsklinikum Düsseldorf 40225 Düsseldorf Tel.: 0211-8106109 Email: n.bittner(a)fz-juelich.de<mailto:n.bittner@fz-juelich.de> ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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matlab crashes on selxavg
by S.V.Shepherd [work] 20 Jun '16

20 Jun '16

Hello, When running more than 3 analyses in parallel in FreeSurfer 5.3, I am getting matlab crashes. Mathworks has politely declined to provide support unless I can replicate outside FsFAST. The errors are variants of """ OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable [...] MATLAB is exiting because of fatal error Killed ------------------------------------------ ERROR: fast_selxavg3() failed\n """ thread_monitor Resource temporarily unavailable in pthread_create *** glibc detected *** /usr/local/MATLAB/R2015b/bin/glnxa64/MATLAB: double free or corruption (!prev): 0x00007f585308c390 *** Segmentation fault (core dumped) """ I have copied Matlab version info below. Any tips on how to troubleshoot? ---------------------------------------------------------------------------------------------------- MATLAB Version: 8.6.0.267246 (R2015b) MATLAB License Number: 1098672 Operating System: Linux 2.6.32-573.18.1.el6.x86_64 #1 SMP Wed Jan 6 11:20:49 EST 2016 x86_64 Java Version: Java 1.7.0_60-b19 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode ---------------------------------------------------------------------------------------------------- MATLAB Version 8.6 (R2015b) Computer Vision System Toolbox Version 7.0 (R2015b) Image Processing Toolbox Version 9.3 (R2015b) Optimization Toolbox Version 7.3 (R2015b) Signal Processing Toolbox Version 7.1 (R2015b) Statistics and Machine Learning Toolbox Version 10.1 (R2015b) *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7699

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Re: [Freesurfer] Hippocampal subfields error
by June Kang 20 Jun '16

20 Jun '16

I am also experiencing same problem. I tried to change ct., but when I change the extension to ctf,It also give errors as below. Error:CTF file '/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' failed to open for 'Read' access. Error message: 'Open a zip file for read/modify failed.' Ubuntu 14.04, nightly dev. version of freesurfer.I also use several mac on 10.9~10.10.5, but they all works well with new hippocampal subfields segmentation function in latest dev. version. June. On Jun 17, 2016, at 2:01 AM, Greenberg, Jonathan <JGREENBERG5(a)mgh.harvard.edu> wrote:Thanks. Has anyone else encountered this error message or knows how it can be solved? Thank you Jonathan ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis [MHIBERT(a)mgh.harvard.edu] Sent: Thursday, June 16, 2016 12:44 PM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfields error No, I just wanted to mention that in case it helps with troubleshooting what went wrong with the new dev version build. Matt ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan [JGREENBERG5(a)mgh.harvard.edu] Sent: Thursday, June 16, 2016 11:24 AM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfields error Thanks Matt. Did you somehow get it to work or recognize the file without the ctf extension? Thanks Jonathan ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis [MHIBERT(a)mgh.harvard.edu] Sent: Thursday, June 16, 2016 11:10 AM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfields error I've also gotten this error recently, with T1, T2, and combined T1+T2 hippocampal segmentations. It looks like the files exist at /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf exist, they just don't have the ".ctf" file extension. Matt ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan [JGREENBERG5(a)mgh.harvard.edu] Sent: Thursday, June 16, 2016 10:29 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampal subfields error Hi all I ran recon-all on data from about 60 participants pre and post an intervention, with the hippocampal subfields flag (e.g. "recon-all -all -subjid SPS01-1910_pre_lazar -hippocampal-subfields-T1"). The recon-all.log file states that the process finished without errors. However, the hippocampal-subfieldsT1.log indicated the following: "Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf" (see below for the full content of hippocampal-subfieldsT1.log). I tried to run only the hippocampal subfield recon-all again (e.g. "recon-all -s recon-all -all -subjid SPS01-1910_pre_lazar hippocampal-subfields-T1") and received the same error message. I tried to look in the indicated folder ("/autofs/cluster/freesurfer/centos6_x86_64/dev/bin") and found a file named segmentSubjectT1_autoEstimateAlveusML (without the ctf extension). I do not know if this is the source of the problem. My FREESURFER_HOME directory is /autofs/cluster/freesurfer/centos6_x86_64/stable6/. My SUBJECTS_DIR is /autofs/cluster/lazar/Projects/jonathan-miracle/unpacking-dicoms/SUBJECTS_DIR/. Any suggestions? (full hippocampal-subfieldsT1.log below) Thank you! Jonathan hippocampal-subfieldsT1.log content: #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Thu Jun 16 09:58:23 EDT 2016 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Thu Jun 16 09:58:26 EDT 2016 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.

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mri_defacing: a faulty stripping of cortex
by HONG Sujin 20 Jun '16

20 Jun '16

Hello, I'm having a problem to use MRI_defacing (default radius 7), which stripped off some frontal areas as well. Does anyone have any similar problems/solutions? I've increased the radius up to 14, which seems reducing the stripping areas, but still remained this stripping problem within the cortex. Best wishes, Sujin Research fellow, Sujin Hong NRlabs Neuropolitics Research School of Social and Political Science The University of Edinburgh Room 2.03 18 Buccleuch Place Edinburgh EH8 9LN Tel: +44 131 650 6632<tel:%2B44%20131%20650%206632> sujin.hong(a)ed.ac.uk<mailto:sujin.hong@ed.ac.uk> & Edinburgh Imaging The University of Edinburgh Room GU426D Chancellor's Building 49 Little France Crescnet Edinburgh EH16 4SB The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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change the algorithm
by N Saf 20 Jun '16

20 Jun '16

Dear Freesurfer, I wonder if it is possible to segment just one sub-cortical structures like hippocampus by changing the algorithm (e.g. according to spatial prior knowledge divided the image to some sub-images and do analysis just on that sub-image which we sure the hippocampus located)and by that reducing the processing time ? and another general question I have is that in sub-cortical segmentation commands 1to12 commands of -all flag which parameters can I change to affect the outputs? Sincerely, Nazanin

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Using Freesurfer commands in matlab
by HARI GURAGAIN 18 Jun '16

18 Jun '16

Dear Freesurfer, I am using the new development version of freesurfer ( ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev) I am trying to call some of the freesurfer commands like: mri_coreg or some other. When I use the something like the following in Matlab: command='/Applications/freesurfer/bin/mri_coreg' and the below: [status,cmdout]=system(command) It is showing a weird error message like below: ########################################### 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 dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib ########################################### I really don't understand why this error is coming. I have seen people have used the mri_*** commands a lot of times in matlab but unfortunately, it shows the above error in my case. Is it the error from Matlab, freesurfer, mac or something else? Any help in solving this issue will be greatly appreciated. Thank you.

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Re: [Freesurfer] GLM_Fit Question
by Arkadiy Maksimovskiy 18 Jun '16

18 Jun '16

Hi Freesurfers, I am having a similar problem with the FSGD file as the user indicated at this thread: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40599.html I am trying to access the script that Doug wrote in order to fix it, however, the link to download the script does not seem to be working. I was wondering if someone might be able to upload it again. Thank you in advance for your help, Arkadiy

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ERROR: mpr2mni305 failed
by Marita Partanen 17 Jun '16

17 Jun '16

Hi there I running freesurfer-Darwin-lion-stable-pub-v5.3.0 on a Mac 10.10.5. I have run recon-all successfully in the past, but now I am getting an error of mpr2mni305 failed, see transforms/talairach_avi.log This issue appears the same as a recent post http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg47393.html but I couldn't see a solution. Any ideas? Here's the full error log: /Users/ophthalmologylab/Studies/Dyslexia_MRI/Intervention/freesurfer/DEGDY001B/mri /Applications/freesurfer/bin/talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Darwin cfri2163m.bcricwh.lan 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 Fri Jun 17 13:29:22 PDT 2016 mri_convert orig_nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=8.14, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 2.91038e-11, -3.72529e-09) j_ras = (-3.72529e-09, -5.82077e-11, -1) k_ras = (7.27596e-12, 1, -5.82077e-11) writing to talsrcimg.img... Analyze Output Matrix -1.000 -0.000 0.000 126.275; 0.000 -0.000 1.000 -112.522; -0.000 -1.000 -0.000 132.333; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Fri Jun 17 13:29:25 PDT 2016 /Applications/freesurfer/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ target=711-2C_as_mni_average_305 --------------------------------------------------------------------- analyzeto4dfp talsrcimg -O0 -y --------------------------------------------------------------------- $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 17 13:29:25 2016 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 --------------------------------------------------------------------- gauss_4dfp talsrcimg 1.1 --------------------------------------------------------------------- dyld: Library not loaded: /usr/local/gfortran/lib/libgcc_s.1.dylib Referenced from: /Applications/freesurfer/bin/gauss_4dfp Reason: image not found Trace/BPT trap ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133 ERROR: mpr2mni305 execution aborted _________________________________ Marita Partanen, M.Sc., M.Ed. Ph.D. Candidate in School Psychology The University of British Columbia 2125 Main Mall Vancouver, BC V6T 1Z4 partanen(a)alumni.ubc.ca<mailto:partanen@alumni.ubc.ca>

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controlling for ICV in LME
by Clara Kühn 17 Jun '16

17 Jun '16

Dear FreeSurfer experts, I conducted a study with 3 groups of children (2 trainings, 1 control) and I want to analyze them longitudinally with LMEs. While preparing my data 2 topics came up that I would like to know more about. A. controlling for ICV/mean thickness/surface area 1) I want to look at changes in cortical thickness and surface area at the whole brain level. Would I then have to control for mean thickness/ area, respectively, per parcellation? Or rather ICV? 2) Is it the same for looking at changes in thickness and area in different ROIs? 3) Since I have (up to) 3 scans per kid, do I include mean thickness/area/ICV for each scan or should I use it from baseline or a mean of all scans? B. demeaning covariates 1) Is it necessary to demean the covariates? I have not seen any hints on the FS wiki pages about that yet. 2) Would I also have to demean the dependent variable (in my case whole brain cortical thickness/surface area)? Thank you! Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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Freesurfer June 2016