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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

2 4

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

3 3

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

3 5

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.

2 5

Extra-axial CSF and TCV GM
by Crocetti, Deana 19 Nov '18

19 Nov '18

External Email - Use Caution Hi Folks, 1) Can I derive a measure of extra-axial CSF. I realize this must be generated in order to create the boundary between the skull and dura but not sure if this is saved in as one of the labels. 2) To generate a measure for Total Cerebral Volume Gray Matter would I combine the following labels? lhCortex + rhCortex + SubCortGray + CerebellumGM Thank you, Deana ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

2 1

FDR correction
by Laura Ferrero 19 Nov '18

19 Nov '18

External Email - Use Caution Hi, I performed an statistical analysis comparing autism group with control group using volume/area and thickness measures. I found significant differences in some regions but they were not significant after FDR correction. The majority of p-values are really high and only some of them are small, I would like to know is that can affect the result. Additionally, I read that it is interesting to do a power analysis to know the amount of difference that can be detected based on the sample size and I would like to know if it is a good approach to follow trying to explain why some results were not significant after multiple comparison correction. Thank you, Laura

2 1

Pial edition and Intensity Normalization / Control points
by Rosalia Dacosta Aguayo 19 Nov '18

19 Nov '18

External Email - Use Caution Dear Free Surfer team, I have edited the pial surface and I am running: -autorecon-pial. This process is taking its time. Then I will look for intensity normalization and control points. Then I will have to run recon-all -autorecon2-cp -autorecon3. I wonder if: 1. Is there any way to do pial and normalization/control points at the same time, so I only have to run the process one time (speed in it up). 2. Is there any other change I should consider when editing? Best regards, Rosalia

2 1

Error tkmedit
by Rosalia Dacosta Aguayo 19 Nov '18

19 Nov '18

External Email - Use Caution Dear Free Surfer experts, I am trying to load my brainmask and the T1 to make editions but I have a problem I do not know how to solve. I would much appreciate your helping here. Best regards, Rosalia *Problem: * ms_naroa@neuroimagen1:~/Escritorio/subjects_controls$ ls 001 006 013 021 027 031 035 039 047 fsaverage 002 008 014 023 028 032 036 040 betn_controls NN 004 009 015 024 029 033 037 043 correct_errors 005 010 017 026 030 034 038 046 Errors_list.ods ms_naroa@neuroimagen1:~/Escritorio/subjects_controls$ tkmedit 002 brainmask.mgz -aux T1.mgz *ERROR: cannot find subject 002 in /home/ms_naroa/subjects or it is not readable by you*

2 1

Re: [Freesurfer] Segmentation fault
by fsbuild 19 Nov '18

19 Nov '18

External Email - Use Caution Hello Jon, Can you get any stack or backtrace information after the segfault occurs ?, e.g., Mac OS has the option to display the crash report with a trace.  On Linux you could run thru gdb and get a back trace.   This would help us to see where the code is exiting..

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