Freesurfer

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30080 discussions

Confusion about PATH/sub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file.
by 周冬跃 23 Sep '21

23 Sep '21

External Email - Use Caution Dear FreeSurfer experts:I use the command recon-all qcache to get file sub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file.And I am confused that the cortical thickness in this file is measured in common space after sub is aligned with the common coordinate system or just measured in subject space after changing the vertex location in subject space?In other words, when a sub is aligned to the common coordinate system,the folding patterns changed.But I am not sure if the value of cortical thickness measures has been changed during this process?

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QDEC command not found
by Fabiola Macruz 23 Sep '21

23 Sep '21

External Email - Use Caution Dear freesurfer experts, I have installed the freesurfer version 7.1.1 in my computer (Mac). After running the longitudinal pipeline in all the patients, I tried to open qdec for the analysis by typing qdec and the answer is "command not found". Could you help me, please? Many thanks, Dra. Fabíola Macruz MD from Faculdade de Ciências Médicas da Santa Casa de São Paulo PhD from Universidade de São Paulo Former Research Fellow from Stanford University Former Clinical Innovation Fellow/ Project Leader from Mass General Brigham Phone: + 1(650)686-0668 / + 55(11)99571-5906

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Freesurfer version confusion
by Paul, Rahul 23 Sep '21

23 Sep '21

Hi freesurfer experts, I was using FreeSurfer v6 for my research. Recently, I started move to FreeSurfer v7.2. I encountered the following issue: Some patients, that had extra large error (xL error), were running fine (recon-all) in freesurfer 6 (it took time, but the process finished, and the segmentation was fine too) but in freesurfer 7, same patient recon-all encountered the extra large error (e.g., CORRECTING DEFECT 35 (vertices=9718, convex hull=1801, v0=40087 Command terminated by signal 11) and after couple of hours recon-all exited (recon-all -s 8375 exited with ERRORS ). I am not sure why recon-all is existing for freesurfer 7.2 and how can I stop that. Thank you Rahul

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mri_glmfit 0 voxels in mask ERROR
by Tsiknia, Amaryllis 23 Sep '21

23 Sep '21

External Email - Use Caution Dear Freesurfer Team, I have been struggling with an error using the mri_gmfit command. I have been trying to run a simple surface-based group analysis on 28 subjects testing whether a continuous variable "OMEGA3_457" relates to various RSI measures while adjusting for the effects of gender. This is the error I am getting: [Image preview] and attached is my .fsgd file. The matrix file I am using is testing for the following contrast: 0 0 0.5 0.5. I produced the lh.N0s2_e4pos.10.mgh file using the mri_surf2surf command after using mri_concat to concatenate the RSI data for all 28 of our subjects into a single lh.N0s2_e4pos.00.mgh file. I have also attached the text file (containing all the paths to the subject data) that was fed into the mri_concat command. Any help would be immensely appreciated. Thank you, Amaryllis A. Tsiknia Imaging Researcher Department of Neurosciences University of California, San Diego atsiknia(a)health.ucsd.edu

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Best graphics card for freesurfer?
by Falko Mecklenbrauck 23 Sep '21

23 Sep '21

External Email - Use Caution Hello Freesurfer Developers, the old Linux-Computer Freesurfer was running on broke down and now we need to buy a new one. The recommondations in the systems requirements were very helpful, but they seem a bit outdated. For Graphics Card it says: * /ATI (AMD) vs nVidia: We still spec nVidia because we don't have problems with its OpenGL-X driver under linux. Perhaps ATI has finally supplied one that works, but this hasn't been attempted in a couple years. ATI cards on the Mac work fine with freesurfer though. /// * /GPU: We no longer support [further] CUDA or GPU development because of lack of resources and difficulty, in preference to using OpenMP, which uses CPU cores. We will continue to support the existing GPU CUDA code that runs on recon-all with the -use-gpu switch. By support, keeping it running with each new nvidia cuda driver release as best as we can./ Is this still accurate? The Tech support at my university would order an AMD graphics card, since the issue with the drivers for Linux seems to be fixed. Does anyone has any current experiences with AMD vs. nVidia graphics cards? Thanks in advance and best wishes, Falko

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Confusion about PATH/sub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file.
by 周冬跃 23 Sep '21

23 Sep '21

External Email - Use Caution Dear FreeSurfer experts: I use the command recon-all qcache to get file sub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file. And I am confused that the cortical thickness in this file is measured in common space after sub is aligned with the common coordinate system or just measured in subject space after changing the vertex location in subject space? In other words, when a sub is aligned to the common coordinate system,the folding patterns changed.But I am not sure if the value of cortical thickness measures has been changed during this process? Best wishes！

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thesegment_T1.sh error
by Szulia Agata 23 Sep '21

23 Sep '21

External Email - Use Caution Hi, I’m trying to run thesegment_T1.sh command on centos 7 in docker (fs 7.2.0). I have matlab v2014b installed in fs there. The subjects were successfully put through recon-all on mac Big Sur (also fs 7.2.0 but matlab does not want to work with Big Sur). I don’t know what to do with the error I get with every recon-all’d subject: Smoothing mesh collection with kernel size 0.750000 ...Smoothing class: 0 /usr/local/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 40: 797 Killed /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML bmat1 /usr/local/freesurfer/subjects 0.333333333333333333333333333333333333 /usr/local/freesurfer/average/HippoSF/atlas/AtlasMesh.gz /usr/local/freesurfer/average/HippoSF/atlas/AtlasDump.mgz /usr/local/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 '/usr/local/freesurfer/bin/fs_run_from_mcr /usr/local/freesurfer/bin/' 0 Linux 3520b46e7a14 5.10.47-linuxkit #1 SMP Sat Jul 3 21:51:47 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Thu Sep 16 23:20:28 UTC 2021 For more details, see the log file /usr/local/freesurfer/subjects/bmat1/scripts/hippocampal-subfields-T1.log If any one of you has run into this kind of problem or know how to solve it, I’d be happy to hear your thoughts. Kind regards, Agata Klauzula poufności. Ta wiadomość pocztowa i wszelkie załączone do niej pliki są poufne i podlegają ochronie prawnej. Jeśli nie jesteś jej prawidłowym adresatem, jakiekolwiek wykorzystanie w tym zapoznanie się z treścią przesłanych informacji, jej ujawnienie, reprodukcja, dystrybucja lub inne rozpowszechnienie, są ściśle zabronione. Jeśli otrzymał/a Pan/i niniejszy przekaz wskutek błędu, proszę o niezwłocznie powiadomienie nadawcy i usunięcie otrzymanych informacji. Kontakt: Uniwersytet Medyczny w Łodzi, 90–419 Łódź, Al. Kościuszki 4, Rektorat – Centrala, Tel. 42 272 59 66 umed.lodz.pl Confidentiality Notice - This e-mail is confidential, may be legally privileged. If you are not the intended recipient, you may not use, disclosure, distribute, copy, print or rely on this e-mail. If you received this e-mail in error, please notify the sender and delete the material from any computer.Contact:Medical University of Lodz, 90–419 Lodz, POLAND, 4 Kosciuszki Avenue, Rector’s Office, phone 0048 42 272 59 66 umed.lodz.pl

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Brainstem segmentation
by Erik O'Hanlon 23 Sep '21

23 Sep '21

External Email - Use Caution Dear Experts, We hope to acquire some multishell dwi and structural data to investigate tracts passing through the Locus Coeruleus (LC) and we want to apply the brainstem segmentation to our structural data to obtain subject specific LC masks. Is it possible to feed multispectral data into the brainstem segmentation ? Is it possible to acquire a high res volume capturing the LC in greater detail and co-register that to the whole brain T1 (T2 or FLAIR ) to further assist in the delineation of the LC roi and quantification of the LC volume? If it's possible to use an additional small volume like this, do I need to pre-process it using recon-all and what is the optimal way to co-register the small volume to the whole brain T1 to assist in the mask generation? Any guidance is very much appreciated. Best regards and thanks, Erik

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Re: [Freesurfer] Best graphics card for freesurfer?
by fsbuild 23 Sep '21

23 Sep '21

External Email - Use Caution Freesurfer dropped support for CUDA builds because it’s too much work to keep up with the compatible combinations of machines, graphics hardware and supported CUDA drivers. Freeview depends upon graphics packages such as Qt and VTK.  My understanding is those packages can make use of OpenGL if the version is recent enough.   That being said, I thought I read VTK may drop OpenGL in version 8 or future versions (freeview currently uses vtk version 7).  Looks like it is worthwhile to use a graphics card that supports OpenGl version 3 or higher (maybe the newest version is up to 4.X ?).  The version numbers for OpenCL may be different and I don’t recall what those are up to now.  But supporting the newer version of those should be preferable on linux machines. For MacOS, graphics cards need to support Apple's Metal Framework (since Mojave, 10.14.X) and OpenGL has been deprecated.   Apple stopped providing Nvidia with the information needed to create Mac graphics drivers and currently uses AMD cards.  Consequently only older/used Nvidia cards work with MacOS which I suspect support only old versions of OpenGL.  So if you have a Mac that allows you to install a graphics card (or you build a Hackintosh), then Nvidia cards are not the most up to date choice and you could be better off with AMD hardware. - R. On Sep 23, 2021, at 02:45, Tim Schäfer <ts+ml(a)rcmd.org> wrote:       External Email - Use Caution        FreeSurfer does not require any special graphics card, you can chose whatever card you like (as long as it works under Linux, but I haven't come across one that did not in the last 10 years or so).*If* you want to run stuff on the GPU (the current FreeSurfer version does not support it afaik, but maybe you have other use cases), an Nvidia card may be better because from what I am seeing, CUDA seems to be more widely used than OpenCL.. If you do not care about CUDA or have never used it, chances are high you can completely ignore this.Tim--Dr. Tim SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe University Frankfurt am Main, GermanyOn 09/23/2021 8:24 AM Falko Mecklenbrauck <f_meck01(a)uni-muenster.de> wrote:External Email - Use Caution        Hello Freesurfer Developers,the old Linux-Computer Freesurfer was running on broke down and now we need to buy a new one.The recommondations in the systems requirements were very helpful, but they seem a bit outdated.For Graphics Card it says: * /ATI (AMD) vs nVidia: We still spec nVidia because we don't have   problems with its OpenGL-X driver under linux. Perhaps ATI has   finally supplied one that works, but this hasn't been attempted in a   couple years. ATI cards on the Mac work fine with freesurfer though. /// * /GPU: We no longer support [further] CUDA or GPU development because   of lack of resources and difficulty, in preference to using OpenMP,   which uses CPU cores. We will continue to support the existing GPU   CUDA code that runs on recon-all with the -use-gpu switch.. By   support, keeping it running with each new nvidia cuda driver release   as best as we can./Is this still accurate? The Tech support at my university would order an AMD graphics card, since the issue with the drivers for Linux seems to be fixed. Does anyone has any current experiences with AMD vs. nVidia graphics cards?Thanks in advance and best wishes,Falko_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/189fIHec85ki6s0KWAB8pP0oKbiWM98vMQvUR7KL50rrGtrfLEEZXBmr9o7be1wSJiTIal_88FuYfZfyDT70uo8dYblkZ-Say_i8LTZ2-tJpp3QxPmW6XME-4L07AUDBsQ30IQJYMtqn8PprlxCcWJ4iAEde1OCTp6sJWJs76sgrPZiCVXCugOu3sXfw8HEt5sCfVpT-wvSN7Z9IC9eROxTMmo_u71DNSxG9cK2yFwbfy5eKPvnrNl08VgMO9kj4Oo6iN25e3VjGw8_--UnwCZQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Notes on running freesurfer on MacOS (including M1 Macs running MacOS BigSur 11.6)
by fsbuild 22 Sep '21

22 Sep '21

External Email - Use Caution There have been various postings to the freesurfer mail list about issues running freesurfer on MacOS including M1 Macs.  The information below may help with running freesurfer (Intel) binaries on MacOS including M1 Macs running BigSur (MacOS 11.6). APPLICATION SANDBOXING The privacy and security features introduced with macOS Mojave (10.14.X) and subsequently expanded in MacOS Catalina (10.15.X) and BigSur (11.X) means that after installation, binaries and applications are by default “sandboxed” and not allowed access to the disk, networked volumes, etc. - unless they are given permission.  Permission should only need to be granted once, but this can be cumbersome if many binaries each need permission to run (compared to a single *.app application bundle). The System Preferences GUI can be used to grant disk access to an individual application (bundle): • Open System Preferences • Click the Security & Privacy tab • Click the Privacy tab • On the left hand side menu scroll to and select Full Disk Access  • Click on the (Locked) padlock in the lower left hand corner and enter your password to unlock it • Click the + button under the list of applications in the right hand side menu; navigate using the Finder to the application you want to grant full disk access to; select it; hit the open button           - OR - it may just work to directly drag the application from a Finder window into the right hand side menu • Make sure the box is checked next to the application you added        • Click on the padlock icon to lock out changes The next time you launch the application, it should have full disk access. So for example you could do the above for the freeview application installed by the freesurfer 7.2.0 Mac installer package as /Applications/freesurfer/7.2.0/Freeview.app Since the binaries and scripts located under /Applications/freesurfer/7.2.0/bin are usually run from the command line using the terminal application, then one option is to grant full disk access to the terminal application.  If you are comfortable with the security risk this poses, then you can use the steps above to navigate to and add /System/Applications/Utilities/Terminal.app to the list of applications with full disk access. FREESURFER LICENSE FILE The format of older freesurfer license files may cause a runtime error, e.g., segfault on MacOS.  Getting a new license file from https://secure-web.cisco.com/12l_F8Ih5rTrxaLIJ9zBhopFqvQieAKP4Zwl… prevent this error. You can set the environment variable FS_LICENSE to set the path to the license file.  For example, if you set that path to be $HOME/license.txt, then there is no need to use sudo/admin privileges to place a license file in an installed freesurfer distribution under /Applications. … assume you downloaded license.txt to your Downloads folder … $ cd $HOME$ pwd/Users/myuid$ cp -p -f  ~/Downloads/license.txt .$ export FS_LICENSE=$HOME/license.txt   <— add appropriate export to your shell init file for whatever shell you set the Terminal.app to run MATLAB INSTALLATION ON M1 MACS The Freesurfer 7.2.0 distribution includes the script /Applications/freesurfer/7.2.0/bin/fs_install_mcr to install the Matlab R2014b run time environment.  While the 7.2.0 release was built and tested with R2014b, this release is too old to be supported on M1 Macs and may cause run time errors.  This will be addressed in a future freesurfer release. RUNNING INTEL BINARIES ON M1 MACS The Freesurfer distribution is currently Intel binary only. Apple provides the built-in Rosetta2 emulation environment to translate applications built for Intel (x86_64) to run on the the M1 hardware (arm64) in real-time.   Or the system detects "on the fly" if the binary is built for x86_64, and then automatically runs Rosetta2 to translate the x86_64 instructions to arm64 instructions and runs them on the M1 chip.  The translation process may take longer for some binaries compared to others. On an M1 Mac, when you open the terminal window and see the shell prompt, you are by default running the arm64 version of zsh.  As soon as you give a command to launch/run an Intel binary, Rosetta2 kicks in with the translation process. While existing freesurfer bash scripts should run under zsh, it is always a safe bet to run the bash shell directly (which was the default shell in older versions of MacOS), e.g, $ bashThe default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://secure-web.cisco.com/1TigoRcERtPmZkpJ6sxYFviEuJi8tV7Pra3nnLa084_Ifz…. … reset the SHELL environment to reflect bash ... userid@developer-Mac:~> export SHELL=/bin/bashuserid@developer-Mac:~> echo $SHELL/bin/bash If you prefer bash, it’s easier to set that as your default shell via the command line or via the GUI.  See https://secure-web.cisco.com/1o3TF1SnLqZ2Nuh7KR_hCEb7CbWPiG-so7-EcBQa_435qUtUZOV5N10jQiqNbIWApj82tKUofowFBi6fVCQ6beS1WFS2zcHWwkjtYYvRLVuHDt97h9Jd15LrTLjK5zjC37l2Oi4fieu_Vdktj1bxiScIAqIpHYyVJtmh9kEdQH8pHpS5XLdlc0oWXoVCejhSqNLiCqwwbpwXeKSNsLO2Uq--t7RIitLhN5Z3UDm7O3dpYs68hs-mdTXAmS-v9f_m0LQ-aQA365l3F8FUhYfv36A/https%3A%2F%2Fsupport.apple.com%2Fen-us%2FHT208050%C2%A0%28e.g., change /bin/zsh to /bin/bash). Users who only want to run Intel binaries sometimes go a step further.  Instead of running the arm64 version of “/bin/bash” (which allows for running both arm64 binaries and x86_64 binaries via Rosetta2 from the same parent shell), they instead directly run the Intel version of “/bin/bash” by invoking bash as, $ arch -x86_64 /bin/bash When running the x86_64 version of a shell then only Intel binaries can run as child processes. - R.

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