Freesurfer February 2020

freesurfer@nmr.mgh.harvard.edu

96 participants
143 discussions

Segmentation problem
by Marina Fernández 27 Feb '20

27 Feb '20

External Email - Use Caution Dear Freesurfeer experts, After running the recon-all, a part of the temporal lobe of one subject was removed. I used the watershed algorithm to be less agressive in the skull stripping step: recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001 And the problem was solved in the brainmask.mgz volume because I can see the temporal lobe completely, but the surfaces are still displaced. In order to correct the surfaces I used the white matter edit tool but there is no change after correcting WM and running the recon-all -autorecon2-wm -autorecon3. I also used control points and but the following error was shown in the terminal when I run the recon-all -autorecon2-cp -autorecon3: recon-all -s sub_001 existed with errors I detected that there are very high values in the white matter of this part of the temporal lobe (even 132), maybe it has something to do. What can I do to solve the problem with this subject? Thank you very much in advance. Best regards, Marina.

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Re: [Freesurfer] Setting up Freeview on Ubuntu Linux 18.04: freeview can't find libpng12
by fsbuild 26 Feb '20

26 Feb '20

External Email - Use Caution You also see a list of packages to install on the freesurfer wiki pages under, https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements - R. On Feb 26, 2020, at 12:03, Tim Schäfer <ts+ml(a)rcmd.org> wrote:       External Email - Use Caution        Hi Tim,try: wget http://mirrors.kernel.org/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1u… dpkg -i libpng12-0_1.2.54-1ubuntu1_amd64.debMore details at https://www.xsmd.org/brain/2019/06/19/freeview-libpng12-so-0-missing-under-…. Tim SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe University Frankfurt am Main, GermanyOn February 26, 2020 at 5:36 PM "Harrigan, Timothy P." <Timothy.Harrigan(a)jhuapl.edu> wrote:       External Email - Use Caution        HI,I'm setting up freeview on a Linux 18..04 system and running through the instructions inhttps://surfer.nmr.mgh..harvard.edu/fswiki/DownloadAndInstallI got through to Example 4: "View the output volumes..."  and got the error below.harritp1@TPHTVB:~/FSSubjects$ freeviewfreeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directoryIt looks like I need to either set up an environment variable, or install that specific graphics library. I did an install of the latest version of libpng: i. e.  sudo apt-get install -y libpng-dev but that didn't fix the problem.Have you dealt with this?ThanksTimTimothy P. Harrigan ScDResearch and Exploratory Development DivisionJohns Hopkins University Applied Physics LaboratoryPhone: 240-228-5943Cell/Text: 240-280-9444_______________________________________________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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Setting up Freeview on Ubuntu Linux 18.04: freeview can't find libpng12
by Harrigan, Timothy P. 26 Feb '20

26 Feb '20

External Email - Use Caution HI, I'm setting up freeview on a Linux 18.04 system and running through the instructions in https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall I got through to Example 4: "View the output volumes..." and got the error below. harritp1@TPHTVB:~/FSSubjects$ freeview freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory It looks like I need to either set up an environment variable, or install that specific graphics library. I did an install of the latest version of libpng: i. e. sudo apt-get install -y libpng-dev but that didn't fix the problem. Have you dealt with this? Thanks Tim Timothy P. Harrigan ScD Research and Exploratory Development Division Johns Hopkins University Applied Physics Laboratory Phone: 240-228-5943 Cell/Text: 240-280-9444

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Re: [Freesurfer] Qdec not running ("image not found" error message)
by fsbuild 26 Feb '20

26 Feb '20

External Email - Use Caution Hello Alex, It looks like you need to install Xquartz on your Mac with the X Windows libraries including libGLU.1.dylib. Download from here, open and run the installer package. https://www.xquartz.org/ - R. On Feb 25, 2020, at 23:27, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience <ladn(a)email.gwu.edu> wrote:        External Email - Use Caution        Dear Freesurfer experts, Please help me with this simple error for running Qdec: - First I try to open qdec: qdec &- Then this occurs: Library not loaded: /opt/X11/lib/libGLU.1.dylib  Referenced from: /Applications/freesurfer/bin/qdec.bin  Reason: image not foundAbortAny ideas on how I could fix this? Thanks! All the best, Alex _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Qdec not running ("image not found" error message)
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 25 Feb '20

25 Feb '20

External Email - Use Caution Dear Freesurfer experts, Please help me with this simple error for running Qdec: - First I try to open qdec: qdec & - Then this occurs: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/bin/qdec.bin Reason: image not found Abort Any ideas on how I could fix this? Thanks! All the best, Alex

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why topology fix almost takes 4 days to finish job
by Frank Robert 25 Feb '20

25 Feb '20

External Email - Use Caution Hello freesurfer experts I am using freesurfer to run recon-all, recon-all -i T1_MPRAGE image -t2 T2-FLAIR-Image It takes about 5 days to finish the process. I find that the most time consuming process is topology fix, it almost takes 4 days for L and R side of hemisphere. I checked the manual, it is supposed to take 1-9h to finish. Do you know why? I think my data set may have a relatively large ventricles ( of course, it is not so large). I put the flags --bigventricles and --parallel, it still takes about 3 days to finish. but if I use recon-all -i T1_MPRAGE image rather than recon-all -i T1_MPRAGE image -t2 T2-FLAIR-Image. It will take about 15h, why this make such big difference? Many thanks. Frank

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Read Freesurfer surfaces and annotation files in C++
by Michael Jordan 25 Feb '20

25 Feb '20

External Email - Use Caution Hi, there are some easy to use Matlab/Python functions to read/write native Freesurfer files (.annot, surfaces etc.) available. Anyone knows something similar for C++ (VTK)? Thank you.

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Question about skull strip error
by Vicky Shi 25 Feb '20

25 Feb '20

External Email - Use Caution Dear Freesurfer expert, I ran recon-all on one subject and part of the cortex was excluded. I followed the FS tutorial to change the watershed preflooding height percentage by using the command below: recon-all -skullstrip -wsthresh 30 -clean-bm -subjid <subject name> The new brainmask file did include all cortex but contain some non-brain tissue (tissue around spinal cord) as well. Then I want to regenerate the aseg.mgz file. So I redo the recon-all command like below: recon-all -all -subjid <subject name> The brainmask output was still like the old one, excluding part of cortex. The new reconstruction seems not use my edited brainmask.mgz. My question is: Do I need to add some flag in recon-all to make sure it use new watershed value/ edited brainmask.mgz? And how I can exclude the non-brain part in the brain mask while keeping all brain part? Simply changing the watershed value didn't do the work well. Thank you so much for your help! Vicky

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lme models time or time^2
by Knut J Bjuland 25 Feb '20

25 Feb '20

External Email - Use Caution Dear FreeSurfer expert I have a lme model with 3 timelines where one timeline is baseline. I two models y = intercept + time + group + sex + time_at_baseline and y = intercept +time +time² + group + sex +time_at_baseline Both time² and time is significant after FDR. How can I decide which model is best? Knut Jørgen Bjuland

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Cannot allocate memory
by Gabriel Tapia 25 Feb '20

25 Feb '20

External Email - Use Caution Hello dear Freesurfer developers, nice to e-meet you and thank you for working on this open source software! I am trying to produce a 3D file of a brain. The command I am trying to run is recon-all and here is the error I get: *CORRECTING DEFECT 57 (vertices=33394, convex hull=9966) Excessive topologic defect encountered: could not allocate 140742253 edges for retessellation Cannot allocate memory* The version I am using is: freesurfer-Linux-centos4-stable-pub-v5.3.0 The platform is Red Hat 64-bit running in a Virtual box with 7835mb allocated memory. You will find the corresponding log file attached. Isn't it surprising that I don't have enough memory with 7835mb allocated? Sorry, I am new to Freesurfer and there might be something I didn't get. Thank you very much in advance for your help, Regards, Gabriel Tapia <https://gabrieltapia.fr/> www.Partage3D.fr <http://partage3d.fr/> +33 6 62 90 11 67

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Freesurfer February 2020