Freesurfer

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30076 discussions

Thalamic segmentation error
by Alan Francis 19 Oct '22

19 Oct '22

External Email - Use Caution Hi Eugenio - Hope all is well. I am running FS 7.2. I have installed the MATLAB Runtime 2014b. However when I run the thalamic segmentation routine I get this error. Please help. Thanks, Alan copernicus:~/IMAGING> segmentThalamicNuclei.sh 973770 Setting ITK threads to 1 #-------------------------------------------- #@# Thalamic Nuclei processing Tue Oct 18 12:25:06 PM CDT 2022 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/MCRv84//runtime/glnxa64:/usr/local/freesurfer/MCRv84//bin/glnxa64:/usr/local/freesurfer/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64: /usr/local/freesurfer/bin/SegmentThalamicNuclei: error while loading shared libraries: libicudata.so.52: cannot open shared object file: No such file or directory Command exited with non-zero status 127 @#@FSTIME 2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 e 0.01 S 0.00 U 0.00 P 33% M 2256 F 11 R 621 W 0 c 1 w 25 I 1776 O 0 L 0.69 0.22 0.07 @#@FSLOADPOST 2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 0.69 0.22 0.07 127 Linux copernicus 5.15.0-50-generic #56-Ubuntu SMP Tue Sep 20 13:23:26 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Thalamic nuclei exited with ERRORS at Tue Oct 18 12:25:06 PM CDT 2022 For more details, see the log file /home/alanfrancis/IMAGING/FREESURFER_SUBJECTS//973770/scripts/thalamic-nuclei-mainFreeSurferT1.log -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*

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mghread : cannot open the file
by priya padma 19 Oct '22

19 Oct '22

External Email - Use Caution Hello Team, I am trying to find the volume of WM, GM, CSF separately and I came across this command namely "mri_compute_volume_fractions" Looking through all the email archives I gave the following line as the command after setting the paths $ mri_compute_volume_fractions --o test --regheader tester /mri/norm.mgz but I get the following error user-MacBook-Pro:sub-AD003S1059S61129 user$ mri_compute_volume_fractions --o test --regheader tester /mri/norm.mgz supposed to be reproducible but seed not set 7.3.2 sysname Darwin hostname user-MacBook-Pro.local machine x86_64 user <username> setenv SUBJECTS_DIR /Applications/freesurfer/7.3.2/subjects cd /Applications/freesurfer/7.3.2/subjects/sub-AD003S1059S61129 mri_compute_volume_fractions --o test --regheader tester /mri/norm.mgz outstem test regfile (null) regtype 0 segfile aseg.mgz wsurf white psurf pial TempVolFile /mri/norm.mgz USF 2 Reading in aseg and surfs from /Applications/freesurfer/7.3.2/subjects/tester Loading /Applications/freesurfer/7.3.2/subjects/tester/mri/aseg.mgz error: mghRead(/Applications/freesurfer/7.3.2/subjects/tester/mri/aseg.mgz, -1): could not open file I set all the paths so why am I not able to read the mgz file? Could anyone help me with this ? Thank you -- Best Regards Padma Priya *AI Developer * *PhenoMx, Inc.* *priya(a)phenomx.ai <priya(a)phenomx.ai> | (+82)10-5405-2685*

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Upgrading Operating System (OS)
by Boa Sorte Silva, Narlon 19 Oct '22

19 Oct '22

External Email - Use Caution Dear FreeSurfer team: I just wanted to confirm the potential issues of upgrading the OS. We are running FreeSurfer 7.1.1 on MacOS 10.4.6 and wanted to upgrade to MacOS 10.15. Our data have been analyzed cross-sectionally and we’ll soon run longitudinal analysis. Would upgrading the MacOS on the same machine and same version of FreeSurfer be detrimental to the analysis results of the same data? In particular, would it bias longitudinal analysis results? Thank you for your help Best regards, Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSHR BC/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon

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trac-all -prep: set: Variable name error
by Ashwati Vipin 19 Oct '22

19 Oct '22

External Email - Use Caution Re-posting this. Please help! Dear Freesurfer Developers, My trac-all -prep with the following command: trac-all -prep -debug -c /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/BIOC_0001_v01_DTI_FS_Sept -no-isrunning |& tee log.txt keeps ending abruptly without any error warning as below: [cid:ce34364b-acd7-48a2-88d6-c8745491c8ab] The subject’s scripts folder still has an IsRunning.trac file. I ran the trac-all -prep command with a debug and have attached the log file for that. I’ve also attached my configuration file. Not sure what’s going wrong? Really appreciate your help! Best, Ashwati Notice: This email is generated from the account of an NUS alumnus. Contents, views, and opinions therein are solely those of the sender.

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Re: [Freesurfer] QXcb connection error 170 (was Freeview: missing voxels in reconstructed surfaces)
by fsbuild 18 Oct '22

18 Oct '22

External Email - Use Caution These errors can happen when the remote machine is running Windows or Linux, but it’s a known issue with some X servers that run on Windows.  When the X windows (graphics/windowing) software trying to remotely display images (which is not freeview) to a machine over the network cannot get the resources it needs, rendering images can be incomplete and report various errors. It could be something is going wrong with trying to remotely render graphics using OpenGL.  You could try setting this to see if it makes a difference, $ export LIBGL_ALWAYS_INDIRECT=0 If you have an IT department, they night be able to help troubleshoot a remote connection.   It could be useful to know that freeview displays images just fine when run directly on the machine you are remotely connecting to -  just as you say it does on your own Mac. - R. On Oct 18, 2022, at 11:32, Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:This appears to be a rendering artifact that happens sometimes with remote display. Are you viewing remotely from a Windows machine?RuopengOn Oct 18, 2022, at 9:45 AM, Sarah Lavelle <lavells1(a)tcd.ie> wrote:        External Email - Use Caution        Dear Freesurfer,I have an issue when viewing my reconstructed surfaces on Freeview my linux version : freesurfer-linux-ubuntu18_x86_64-devfreesurfer 7-devThe surfaces have a large number of empty voxels. This is not a problem with the recon-all function as I can see the same surface file perfectly on my Mac with the fully working mac version. It seems to be a problem with my Freeview.Some additional information that may help finding the cause:When I open Freeview from Ubuntu, I get the following errors:QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-lavells1'QXcbConnection: XCB error: 170 (Unknown), sequence: 174, resource id: 90, major code: 146 (Unknown), minor code: 20QXcbConnection: XCB error: 170 (Unknown), sequence: 174, resource id: 90, major code: 146 (Unknown), minor code: 20There are no other errors in ubuntu after I load Freeview i.e. No errors in Ubuntu when I then load the surface.I hope you can help me fix this issue as soon as possible. Many thanks,Sarah<image.png><Empty_Voxels_PialSurface_CloseUp.PNG><Empty_Voxels_PialSurface.PNG>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] matlab 2019b and brainstem substructures analysis
by fsbuild 18 Oct '22

18 Oct '22

External Email - Use Caution Hello Jung, You can try either matlab R2014b or R2019b with the commands below. You should have already set FREESURFER_HOME in your Environment to point to where it is installed …. I will list a default location here for a linux install but what you set for FREESURFER_HOME should not matter (as long as it is a valid path). $ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0 … then you should run the provided script to install one of the above Matlab environment with either the argument R2014b or R2019b.   You can run the script multiple times to switch between the distributions, but you can only install and use one at a time. $ cd $FREESURFER_HOME/bin$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr  R2014b … switch to R2019b ... $ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr  R2019b I can’t comment on which might be a better choice, but I believe the 7.2..0 release was tested with R2014b, and subsequently the current 7.3.2 release was updated to use and tested with R2019b.   Since you are running 7.2.0, I would try installing R2014b as listed above and running with that. You can find all the 7.X releases under, https://secure-web.cisco.com/1RxNv9aW1kS9fevrfjvWAkwbIG9pgzvcCv… - R. -------- Forwarded Message --------Subject:[Freesurfer] matlab 2019b and brainstem substructures analysisDate: Sat, 8 Oct 2022 17:26:14 +0800From: tulu@ms36.hinet.netReply-To:Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>To: freesurfer@nmr.mgh.harvard.edu        External Email - Use Caution        Dear Freesurfer experts,I will analysis brainstem structure and I use Freesurfer 7.2 version and maltab 2019b.I wonder if I need to install Matlab R2014b runtime or how to run hippocampal subfield/brainstem module by matlab2019b Thanks your helpJung Lung Hsu<Attached Message Part.txt>

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Re: [Freesurfer] 7.2.0 CentOS7 and Ubuntu 18.04
by fsbuild 18 Oct '22

18 Oct '22

External Email - Use Caution Hello Jim, We do post this caveat on the download page, Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). So I suspect the answer is it depends upon what you are running and, e.g., how statistics are subsequently computed using the (floating point) output.   Running on a different OS with a different release of Freesurfer means floating point results will not be identical to the output produced with your previous systems and (older) FS releases at some position to the r.h.s of the decimal point. - R. On Oct 18, 2022, at 11:22, Alexopoulos, Dimitrios <dimitriosalexopoulos@wustl..edu> wrote:        External Email - Use Caution        We’ve made system software upgrades recently and of some our data was run using the FS 7.2.0 CentOS 7 build but on Ubuntu 18.04 servers. The outputs look good and there no output errors. Should these data be rerun? Jim     The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Tracula - Preproc
by Alan Francis 18 Oct '22

18 Oct '22

External Email - Use Caution Hi Anastasia, King Wei: I did as you suggested with the config file and the preprocessing ran for a bit but then an error occurred. I have attached the run script. It says BET not found. Is this the Brain Extraction tool? Could you please shed some light on this? thanks so much, Alan -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*

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Freeview: missing voxels in reconstructed surfaces
by Sarah Lavelle 18 Oct '22

18 Oct '22

External Email - Use Caution Dear Freesurfer, I have an issue when viewing my reconstructed surfaces on Freeview my linux version : freesurfer-linux-ubuntu18_x86_64-dev freesurfer 7-dev The surfaces have a large number of *empty voxels*. This is not a problem with the recon-all function as I can see the same surface file perfectly on my Mac with the fully working mac version. It seems to be a problem with my Freeview. Some additional information that may help finding the cause: When I open Freeview from Ubuntu, I get the following errors: QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-lavells1' QXcbConnection: XCB error: 170 (Unknown), sequence: 174, resource id: 90, major code: 146 (Unknown), minor code: 20 QXcbConnection: XCB error: 170 (Unknown), sequence: 174, resource id: 90, major code: 146 (Unknown), minor code: 20 There are no other errors in ubuntu after I load Freeview i.e. No errors in Ubuntu when I then load the surface. I hope you can help me fix this issue as soon as possible. Many thanks, Sarah [image: image.png] [image: Empty_Voxels_PialSurface_CloseUp.PNG] [image: Empty_Voxels_PialSurface.PNG]

2 1

mris_make_surfaces error: MRISedges(): too many faces
by Arcaro, Michael 18 Oct '22

18 Oct '22

External Email - Use Caution Hey FreeSurfer Devs! I’m trying to do a surface reconstruction on a rodent-sized animal (tree shrew). I have a good segmentation of the white matter and have been able to generate reasonable looking orig / smoothwm surfaces. I’m running into an error with mris_make_surfaces: MRISedges(): too many faces: 9578 9599 n=9, m=4, k=2. I am running this command manually: mris_make_surfaces -noaseg -orig_white lh.smoothwm.nofix -white white.preaparc -noaparc -mgz -T1 brain shrewsurf lh I also hit this error when running autorecon2: recon-all -autorecon2-wm -subjid shrewsurf -hires -nonormalization2 -nofill -noaseg -nosegmentation -nocortribbon -notessellate -no-isrunning Some details on the MRIs I’m trying to do this recon on: 0.05mm^3 T2. No T1s (poor contrast on 9.4T). I’m trying to recon on the native resolution: mris_convert T2.nii T2.mgz -cs 0.05. I dummied a T1 by segmenting the grey/white matter, assigned voxels values of 90 and 110, respectively, then blurred the image a little so there is a gradient across the grey matter from white matter to out of brain. I’ve had no issues running mri_tessellate, mris_extract_main_component, mris_smooth, mris_inflate. Any advice would be greatly appreciated! Mike

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