Freesurfer November 2018

freesurfer@nmr.mgh.harvard.edu

121 participants
189 discussions

nu_correct ERROR (FreeSurfer v6)
by Korom, Marta 20 Nov '18

20 Nov '18

External Email - Use Caution Dear FreeSurfer Developers, I have the most recent version of FreeSurfer installed on a MacOS Mojave (10.14) and as I was running recon-all, I received the following error message: "Assertion failed at line 742 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct Darwin Martas-MacBook-Pro.local 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64 recon-all -s plc0061 exited with ERRORS at Tue Nov 20 22:32:15 EST 2018" I reviewed many threads on the same error message, but none of them were solved. I have the same version of FreeSurfer on two other MacBooks (with older versions of iOS) and both work fine. I ran fixup_mni_paths as it was suggested on multiple threads and nu_correct, as well and I got the following message: "nu_correct nu_correct, version 1.12.0 Usage: nu_correct [-help] [options] in.mnc out.mnc" Any thoughts on what the problem might be and how it could be fixed? Could this be an iOS compatibility issue? Gratefully, Marta -- *Marta Korom | *PhD Candidate University of Delaware, Clinical Science e-mail: mkorom(a)udel.edu phone: 646 861 8461 http://www.abcintervention.org/

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differences between 'lh_G_front_middle_thickness' and 'lh_S_front_middle_thickness'
by charujing123 20 Nov '18

20 Nov '18

External Email - Use Caution Hi FS experts and users I found two middle frontal cortex in thickness, with different prefix. So what is the difference? Another question: Can I get the thickness of hippocampus and amygdala? Thanks. Rujing 2018-11-21 charujing123

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Bonferroni correction of 2spaces or 3spaces
by YAN Chao-Gan 20 Nov '18

20 Nov '18

External Email - Use Caution Dear freesurfer experts, I have a pretty naive question but would like to confirm. When we use --3spaces option in multiple comparison correction, does that mean we set the Cluster-wise threshold (cwp, not Cluster Defining Threshold or Cluster Forming Threshold) to 0.5/3=0.0167 for lh. Similar cwp at 0.0167 for rh and subcortical? In addition, if we use "--cortex" to restrict the calculation on cortex only, where can we find the corresponding mask or label file for cortex? Thanks, Chao-Gan -- Chao-Gan YAN, Ph.D. Professor, Principal Investigator Deputy Director, Magnetic Resonance Imaging Research Center Institute of Psychology, Chinese Academy of Sciences 16 Lincui Road, Chaoyang District, Beijing 100101, China - Initiator <http://rfmri.org/DPARSF>DPABI <http://rfmri.org/DPABI> <http://rfmri.org/DPARSF>, <http://dpabi.org>DPARSF <http://rfmri.org/DPARSF>, PRN <http://rfmri.org/PRN> and The R-fMRI Network <http://rfmri.org> (RFMRI.ORG <http://rfmri.org/>) http://rfmri.org/yan http://scholar.google.com/citations?user=lJQ9B58AAAAJ

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Re: [Freesurfer] License issue
by fsbuild 20 Nov '18

20 Nov '18

External Email - Use Caution Hi Sarah, I would just move that file aside (rename it to something that is not license.txt) and follow the instructions on the wiki to generate another license.txt file.  Then you could check it again with the previous commands. https://surfer.nmr.mgh.harvard.edu/fswiki/License - R. On Nov 20, 2018, at 18:30, Sarah Haigh <shaigh(a)unr.edu> wrote:        External Email - Use Caution        Hi,I ran the code and the license appeared, but no email address or numbers. These were the first few lines:FreeSurfer Software License Agreement ("Agreement")                    Version 1.0 (February 2011)Is this wrong? The rwx settings look correct.ThanksSarah On Nov 20, 2018, at 2:52 PM, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Hello Sarah,If you can bring up a terminal with your freesurfer environment set, then please try the following commands, i.e.,$ cd $FREESURFER_HOME$ cat $FS_LICENSE<output deleted>Without posting the contents of your license, I think the first line is an email address, followed by a line with several numbers, followed by 2 lines of text.$ ls -l $FS_LICENSE-rw-r--r--@ 1 userid  staff  57 Jan  9  2018 /Users/userid/license.txtthe rw-r-r privileges (644) mean its writeable only by you (which is fine).- R.- R.Sarah Haigh November 20, 2018 at 16:42External Email - Use Caution Yes, I set the FreeSurfer home environment and added the license file to that folder. It is Word readable.Sarah_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferGreve, Douglas N.,Ph.D. November 20, 2018 at 15:03did you put it in $FREESURFER_HOME/.license ? Is it world-readable?_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferSarah Haigh November 20, 2018 at 14:38External Email - Use Caution Hello Freesurfers,Can anyone help with a licensing issue I have? I downloaded Freesurfer the other day with a brand new license and got the following message: “ERROR: Invalid FreeSurfer license key was found in license file”. I tried getting a new license and even borrowed someone else’s license and they all came up with the same error. Any ideas?Thanks for your help.Sarah_____Assistant Professor,University of Nevada, Reno,Department of Psychology and Center for Integrative Neuroscience,1664 N. Virginia Street Reno, NV 89557-0296Carnegie Mellon University,Department of Psychology and Center for the Neural Basis of Cognition,5000 Forbes Avenue,Pittsburgh, PA 15213._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&amp;data=01%7C01%7Cshaigh%40unr..edu%7C16c5246a561d4631f7bc08d64f3ae949%7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C1&amp;sdata=W1G8vsv2ubqApboTTM9kTHllGoV%2Bc4aX9gC6sW2fTqI%3D&amp;reserved=0_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] License issue
by fsbuild 20 Nov '18

20 Nov '18

External Email - Use Caution Hello Sarah, If you can bring up a terminal with your freesurfer environment set, then please try the following commands, i.e., $ cd $FREESURFER_HOME $ cat $FS_LICENSE <output deleted> Without posting the contents of your license, I think the first line is an email address, followed by a line with several numbers, followed by 2 lines of text. $ ls -l $FS_LICENSE-rw-r--r--@ 1 userid  staff  57 Jan  9  2018 /Users/userid/license.txt the rw-r-r privileges (644) mean its writeable only by you (which is fine). - R. - R. Sarah Haigh November 20, 2018 at 16:42 External Email - Use Caution Yes, I set the FreeSurfer home environment and added the license file to that folder. It is Word readable. Sarah _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Greve, Douglas N.,Ph.D. November 20, 2018 at 15:03 did you put it in $FREESURFER_HOME/.license ? Is it world-readable? _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Sarah Haigh November 20, 2018 at 14:38 External Email - Use Caution Hello Freesurfers, Can anyone help with a licensing issue I have? I downloaded Freesurfer the other day with a brand new license and got the following message: “ERROR: Invalid FreeSurfer license key was found in license file”. I tried getting a new license and even borrowed someone else’s license and they all came up with the same error. Any ideas? Thanks for your help. Sarah _____ Assistant Professor, University of Nevada, Reno, Department of Psychology and Center for Integrative Neuroscience, 1664 N. Virginia Street Reno, NV 89557-0296 Carnegie Mellon University, Department of Psychology and Center for the Neural Basis of Cognition, 5000 Forbes Avenue, Pittsburgh, PA 15213. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_glmfit-sim MRISread(?????): could not open file
by C.P.E. Rollins 20 Nov '18

20 Nov '18

External Email - Use Caution Dear Freesurfer Developers, I'm trying to run mri_glmfit-sim to correct for multiple comparisons but am receiving the following error: cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt SURFACE: fsaverage lh log file is lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log cd /home/cper2/BeneMin/Freesurfer /applications/freesurfer/freesurfer_6.0.0/bin/mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache 2 neg --cwp 0.05 --2spaces $Id: mri_glmfit-sim,v 1.66 2016/11/16 20:52:22 greve Exp $ Fri Nov 16 09:38:40 GMT 2018 Linux wbic-gate-2 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) x86_64 GNU/Linux cper2 setenv SUBJECTS_DIR /home/cper2/BeneMin/Freesurfer FREESURFER_HOME /applications/freesurfer/freesurfer_6.0.0 Original mri_glmfit command line: cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 26.134985 CSD /applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/neg/th20/mc-z.csd mri_surfcluster --in lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh --mask lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.mgh --sum lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.summary --ocn lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.masked.mgh --no-fixmni --csd /applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/neg/th20/mc-z.csd --csdpdf lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.pdf.dat --vwsig lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.voxel.mgh --vwsigmax lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.voxel.max.dat --oannot lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.annot --bonferroni 2 --surf white Creating CDFs from CSD files csd->threshsign = -1 thsign = neg, id = -1 version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $ hemi = lh srcid = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = neg thmin = 2 thmax = -1 fdr = -1 minarea = 0 Bonferroni = 2 xfmfile = talairach.xfm nth = -1 outid = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.masked.mgh MGH ocnid = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.mgh MGH sumfile = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.summary subjectsdir = /home/cper2/BeneMin/Freesurfer FixMNI = 0 Found 149955 vertices in mask Found 149955 vertices in mask Found 149955 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /home/cper2/BeneMin/Freesurfer/fsaverage/mri/transforms/talairach.xfm 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; MRISread(?????): could not open file No such file or directory ---------------------------------------------------- Reading source surface /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white mri_surfcluster.bin: could not read surface /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white No such file or directory However, the files /home/cper2/BeneMin/Freesurfer/fsaverage/mri/transforms/talairach.xfm and /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white both exist and I can read them looking at the permissions. I was wondering if you might have any advice for this. Many thanks, Colleen

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License issue
by Sarah Haigh 20 Nov '18

20 Nov '18

External Email - Use Caution Hello Freesurfers, Can anyone help with a licensing issue I have? I downloaded Freesurfer the other day with a brand new license and got the following message: “ERROR: Invalid FreeSurfer license key was found in license file”. I tried getting a new license and even borrowed someone else’s license and they all came up with the same error. Any ideas? Thanks for your help. Sarah _____ Assistant Professor, University of Nevada, Reno, Department of Psychology and Center for Integrative Neuroscience, 1664 N. Virginia Street Reno, NV 89557-0296 Carnegie Mellon University, Department of Psychology and Center for the Neural Basis of Cognition, 5000 Forbes Avenue, Pittsburgh, PA 15213.

2 2

Conversion of surface files to nibabel-readable files
by Borges Pereira Ines Isabel 20 Nov '18

20 Nov '18

External Email - Use Caution Dear FreeSurfer developers, I am trying to segment the cortex of my subjects into multiple layers and am trying several approaches. I have tried the command "mris_expand -thickness lh.white 0.5 lh.graymid" and it works perfectly. I am also interested in trying other approaches from other software packages and have started to experiment with nighres. Is it possible to convert the FreeSurfer surface files (pial and white) to a nibabel SpatialImage format or another format that can be read by the nibabel/nighres python library? I have searched the FreeSurfer documentation but couldn’t find a direct answer. I also see that nibabel has a freesurfer module and hence I am able to load the images to a python script. However, when I attempt to use perform volumetric layering with nighres, it returns a value error, given that the “input volume must be either a path to a file that Nibabel can load or a nibabel SpatialImage." I will also contact the nighres developers but was wondering if Freesurfer already takes into account the possible interaction between different software packages. Many thanks! Best regards, Inês Pereira

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Recon-all - mghRead could not read rawavg.mgz
by Batuhan Erkat 20 Nov '18

20 Nov '18

External Email - Use Caution Hello, I am using FreeSurfer solely for reconstruction. I am having an issue I didn't have a month ago, right at the beginning of reconstruction pipeline. I am using FreeSurfer v5.3.0 on an Ubuntu 14.04 server. Based on some search and thinking, I guess that mghread is not able to read rawavg.mgz either there is a bug with the mghread or the data gets corrupted during mri_convert, because when I inspect the T1.nii images, there seems to be nothing wrong. Furthermore, I tried recon-all command on the anatomical images I reconstructed a month ago without any error (which means they were totally okay), but not surprisingly I received the same error message when I tried to conduct recon-all on them: *mghRead(/auto/data/batuhan/output/BE/mri/rawavg.mgz): could not read 229376 bytes at slice 0* I also included an error log, and the full terminal output where I bolded out the problematic lines. Also, I am not sure how related it is with my issue but there are some warnings from perl as well. -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /auto/data/batuhan/output MNI_DIR /usr/local/freesurfer/mni batuhan@chimere:~$ recon-all -i /auto/data/batuhan/output/BE_T1.nii -s BE -all Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /auto/data/batuhan/output Actual FREESURFER_HOME /usr/local/freesurfer Linux chimere 3.13.0-85-generic #129-Ubuntu SMP Thu Mar 17 20:50:15 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = "en_US:en", LC_ALL = (unset), LC_PAPER = "tr_TR.UTF-8", LC_ADDRESS = "tr_TR.UTF-8", LC_MONETARY = "tr_TR.UTF-8", LC_NUMERIC = "tr_TR.UTF-8", LC_TELEPHONE = "tr_TR.UTF-8", LC_IDENTIFICATION = "tr_TR.UTF-8", LC_MEASUREMENT = "tr_TR.UTF-8", LC_TIME = "tr_TR.UTF-8", LC_NAME = "tr_TR.UTF-8", LANG = "C" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). /auto/data/batuhan/output/BE mri_convert /auto/data/batuhan/output/BE_T1.nii /auto/data/batuhan/output/BE/mri/orig/001.mgz mri_convert /auto/data/batuhan/output/BE_T1.nii /auto/data/batuhan/output/BE/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /auto/data/batuhan/output/BE_T1.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, 1) k_ras = (1, 0, 0) writing to /auto/data/batuhan/output/BE/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Fri Nov 16 23:43:47 +03 2018 Found 1 runs /auto/data/batuhan/output/BE/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /auto/data/batuhan/output/BE/mri/orig/001.mgz /auto/data/batuhan/output/BE/mri/rawavg.mgz /auto/data/batuhan/output/BE mri_convert /auto/data/batuhan/output/BE/mri/rawavg.mgz /auto/data/batuhan/output/BE/mri/orig.mgz --conform *mri_convert /auto/data/batuhan/output/BE/mri/rawavg.mgz /auto/data/batuhan/output/BE/mri/orig.mgz --conform mghRead(/auto/data/batuhan/output/BE/mri/rawavg.mgz): could not read 229376 bytes at slice 0$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $reading from /auto/data/batuhan/output/BE/mri/rawavg.mgz...Invalid argument* Linux chimere 3.13.0-85-generic #129-Ubuntu SMP Thu Mar 17 20:50:15 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s BE exited with ERRORS at Fri Nov 16 23:43:50 +03 2018 For more details, see the log file /auto/data/batuhan/output/BE/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thank you. Best regards, O. Batuhan Erkat -- MSc Candidate Neuroscience Graduate Program National Magnetic Resonance Research Center (UMRAM) & Aysel Sabuncu Brain Research Center Bilkent University Ankara, 06800 Turkey

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Tracula Question-How the threshold in final merged tracts are defined?
by June Kang 19 Nov '18

19 Nov '18

External Email - Use Caution In the visualization step of Tracula processing, freeview -tv merged_avg33_mni_bbr shows some tracts with very high threshold (i.e. 171), which make them look like the reconstruction-failed ones. The tracts failed to reconstruction usually show threshold of 300 (not changeable) with tiny rounded cylinder shape. In successfully reconstructed tracts with very high threshold, it looks ok, when I adjust threshold to the similar value from contralateral one. Is there any reason for this extremely high threshold? or it’s just randomly set values? Bests, J.

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Freesurfer November 2018