Freesurfer October 2023

freesurfer@nmr.mgh.harvard.edu

69 participants
95 discussions

RECON ALL Error
by Massimo Valerio 08 Oct '23

08 Oct '23

External Email - Use Caution Dott. Massimo VALERIO Neuropsichiatra Infantile SSD Neurologia Pediatrica Dipartimento di Patologia e Cura del Bambino Regina Margherita A.O.U Citta della Salute e della Scienza della Citta di Torino Presidio Ospedale Infantile Regina Margherita Piazza Polonia 94, 10126 Torino Tel: 011 3135248 Fax: 011 3135439 Email: massimo.valerio(a)unito.it Il giorno dom 8 ott 2023 alle ore 16:22 Massimo Valerio < massimo.valerio(a)unito.it> ha scritto: > Hello FreeSurfer Developers, > > I'm attempting to compute the recon-all of T1 3D of my patient. > ERROR: > > \n mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta > /Applications/freesurfer/subjects/PZDALENE/mri/transforms/cc_up.lta > PZDALENE \n > > will read input aseg from aseg.auto_noCCseg.mgz > > writing aseg with cc labels to aseg.auto.mgz > > will write lta as > /Applications/freesurfer/subjects/PZDALENE/mri/transforms/cc_up.lta > > reading aseg from > /Applications/freesurfer/subjects/PZDALENE/mri/aseg.auto_noCCseg.mgz > > reading norm from /Applications/freesurfer/subjects/PZDALENE/mri/norm.mgz > > 39269 voxels in left wm, 29817 in right wm, xrange [112, 141] > > searching rotation angles z=[-7 7], y=[ 9 23] > > searching scale 1 Z rot 5.0 global minimum found at slice 127.0, > rotations (14.74, -1.72) > > final transformation (x=127.0, yr=14.745, zr=-1.723): > > 0.96663 0.03006 0.25439 -31.60547; > > -0.02907 0.99955 -0.00765 15.74752; > > -0.25451 0.00000 0.96707 33.63651; > > 0.00000 0.00000 0.00000 1.00000; > > mri_cc: no WM voxels found with norm > 40 -- check skull stripping > > > No such file or directory > > Darwin MBPdiNeirurgia4.fritz.box 21.6.0 Darwin Kernel Version 21.6.0: Fri > Sep 15 16:17:23 PDT 2023; root:xnu-8020.240.18.703.5~1/RELEASE_X86_64 x86_64 > > > recon-all -s PZDALENE exited with ERRORS at Sun Oct 8 02:34:07 CEST 2023 > > > > I've searched the list and no similar errors have been reported. > Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive > attached the recon-all.log in case it's of any use. > > 1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c > 2) Platform: MacOs Monterey 12.7 > 3) uname -a: Darwin MBPdiNeirurgia4.fritz.box 21.6.0 Darwin Kernel > Version 21.6.0: Fri Sep 15 16:17:23 PDT 2023; root:xnu-8020.240.18.703.5~1/RELEASE_X86_64 > x86_64 > 4) recon-all.log: see attached > > > > Dott. Massimo VALERIO > > Neuropsichiatra Infantile > SSD Neurologia Pediatrica > Dipartimento di Patologia e Cura del Bambino Regina Margherita > A.O.U Citta della Salute e della Scienza della Citta di Torino > Presidio Ospedale Infantile Regina Margherita > Piazza Polonia 94, 10126 Torino > Tel: 011 3135248 > Fax: 011 3135439 > Email: massimo.valerio(a)unito.it > > > <https://secure-web.cisco.com/1NNui4wxv6m_TmgOnzlJg9RYl5qaN4AkQ33H4VEWmLcrOo…> Privo > di virus.http://secure-web.cisco.com/1sOwZmGRpeVGH_FSbs-TgSzvLT2A8yzMOa_UqlXrz… > <https://secure-web.cisco.com/1NNui4wxv6m_TmgOnzlJg9RYl5qaN4AkQ33H4VEWmLcrOo…> > <#m_-8264439549155417804_m_3222428717412999766_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >

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fRe: SAMSEG lesion mask pattern on Mac with M2 processor and GPU
by fsbuild 07 Oct '23

07 Oct '23

External Email - Use Caution  Python code  (including 3rd party python packages) in the Intel Mac build cannot be guaranteed to run on Mac M1, M2 arm processors.  Package developers may still build their code using Intel processor specific instructions which cannot be emulated by the Rosetta environment on arm64 Macs.  Rosetta translates Intel processor instructions to arm64 processor instructions; when there is no equivalent arm processor instruction, you get the error “illegal instruction”.  The remedy for this is to re-write and/or re-build the code (to be more portable). There is an arm64 freesurfer development build including an arm64 python with Apple’s tensorflow.   However, the freesurfer python code is not yet entirely compatible with arm64 python and all its packages.  The mri_synthsr script currently does not work with arm64 tensorflow; I don’t know about mri_samseg.   You can try the arm64 development build via the link,  https://secure-web.cisco.com/17oMRv7D8FpOpyCTDI2b6q3ZFH9-liuuaw55Fk0qAsqgBnL3cDmnkVAujZjuxE5eX79DEYS-N-28sS2kPCHZELA_TD9KfXA1gTpkIIQlltrdLjmUYAErTEyV7pXp61dNngBidguhX9Ro7dWKp68cyGlPyIUMglyRLC5Ic8KxVhEd1h6taIbJUs2RF62qX_akkZQzboTafybXKGqtqZO75VJ_VYmF1FbMwq5IEVXbxaM1fZtZ1ZQn6V7EGFGVpOnhJcYCh6SCvDAdGOF8jbC_XE4GUihNWJa4hRA4860MsPxHxc4Or__ON8TElFES-SLctaTntlZ16qO5C18SyRBuAGw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg%26nbsp; Please keep in mind this it not a release build and please report any errors. Fixes for these kinds of issues will become available in the development builds via the link above once they are added into the freesurfer development stream.   We can also notify the list. - R. On Oct 7, 2023, at 03:23, Bianka Forgó <fbia021(a)gmail.com> wrote:        External Email - Use Caution        Dear Freesurfer Developers,I am attempting to use Freesurfer on MacOS Ventura (version 13.5.2) with an M2 Pro silicone chip and GPU. I have successfully installed Freesurfer version 7.4.1.I am trying to use samseg for cross-sectional MS lesion volume analysis by running the following command:run_samseg --input Freesurfer_subjects/T1.nii Freesurfer_subjects/FAMUS/T2FLAIR_reg.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output Freesurfer_subjects/FAMUS/samsegI get the error message:zsh: illegal hardware instruction  run_samseg --input Freesurfer_subjects/FAMUS/T1.nii   --lesion  0 1 As described in the samseg manual, one may be prompted to use Tensorflow when using this module for the first time. I was not prompted to do so but I did install it (and python3 as well) using the instructions here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1tE2yZiNK2sSgfXl2g2jsBKvz4UwOnAafBZo84… this, I still get the above error message.I can also see that there is no support for running Tensorflow on Mac with GPU.Does this mean that there's no way for me to run this command or is there anything else I can try to solve this?Of note, the basic samseg command (run_samseg --input <file> [<file> ...] --output <dir> [--threads <threads>] [--pallidum-separate]) is running without any issues.Thank you,Bianka_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Use of infantFS and FS in the interval 2 - 4.5 years of age
by michefabb 07 Oct '23

07 Oct '23

External Email - Use Caution Dear FS experts, I see it is recommended to use infantFS below 2 years of age, whereas FS has been used for 4.5 years and above. I was wondering what could be used in the interval 2 - 4.5 years of age: which are benefits and drawbacks of both? Thanks, appreciated, Mic

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SAMSEG lesion mask pattern on Mac with M2 processor and GPU
by Bianka Forgó 07 Oct '23

07 Oct '23

External Email - Use Caution Dear Freesurfer Developers, I am attempting to use Freesurfer on MacOS Ventura (version 13.5.2) with an M2 Pro silicone chip and GPU. I have successfully installed Freesurfer version 7.4.1. I am trying to use samseg for cross-sectional MS lesion volume analysis by running the following command: run_samseg --input Freesurfer_subjects/T1.nii Freesurfer_subjects/FAMUS/T2FLAIR_reg.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output Freesurfer_subjects/FAMUS/samseg I get the error message: zsh: illegal hardware instruction run_samseg --input Freesurfer_subjects/FAMUS/T1.nii --lesion 0 1 As described in the samseg manual, one may be prompted to use Tensorflow when using this module for the first time. I was not prompted to do so but I did install it (and python3 as well) using the instructions here: https://secure-web.cisco.com/13jV9GWC39Eu7ptAevMhql74Ty0xCnVcRkXqXbKh6yiJZq… After this, I still get the above error message. I can also see that there is no support for running Tensorflow on Mac with GPU. Does this mean that there's no way for me to run this command or is there anything else I can try to solve this? Of note, the basic samseg command (run_samseg --input <file> [<file> ...] --output <dir> [--threads <threads>] [--pallidum-separate]) is running without any issues. Thank you, Bianka

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Re: [Freesurfer] Free surfer quits unexpectedly
by fsbuild 06 Oct '23

06 Oct '23

External Email - Use Caution  Please try the following, … open a new terminal and run the bash shell … I am cd’d to /tmp though it should not matter ... $ cd /tmp$ 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/1B3JRrCA1-GeI0tKc8qR9oVMx4vfk7xlYLxiqqBDOBuaes… … check the version of Quartz by starting an xterm.  When the xterm window opens check the version from the upper left hand corner XQuartz application pull down menu and check what “About X11” reports.  Check you have Quartz 2.8.2 or later and then quit the xterm window. Mac:/tmp> which xterm/opt/X11/bin/xtermMac:/tmp> xterm & … copy your license.txt file into your home directory.  For example if you downloaded the license by default into your Downloads folder, then copy it from there into $HOME … Mac:/tmp> cd $HOMEMac:~> cp -p -f ./Downloads/license.txt . … set the environment variable FS_LICENSE to point to the license file … later you can put this in your shell init file to be the default when you launch a new terminal window with your default shell …  Mac:~> export FS_LICENSE=$HOME/license.txtMac:~> head -1 $FS_LICENSEyou(a)somedomain.com                   <— email you used to register for the license … setup the freesurfer environment … Mac:~> export FREESURFER_HOME=/Applications/freesurfer/7.4.1Mac:~> source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.4.1FSFAST_HOME       /Applications/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.4.1/subjectsMNI_DIR           /Applications/freesurfer/7.4.1/mni … first check freeview with no arguments opens an empty window … Mac:~>  which freeview/Applications/freesurfer/7.4.1/bin/freeviewMac:~> freeview … close the freeview window and try to open a knoen to be good volume file ... … check the volume file exists … Mac:~> ls -l $SUBJECTS_DIR/bert/mri/T1.mgz-rwxr-xr-x  1 root  wheel  4502402 Jul 13  2021 /Applications/freesurfer/7.4.1/subjects/bert/mri/T1.mgz* … try opening the volume file …Mac:~> freeview $SUBJECTS_DIR/bert/mri/T1.mgz If the above works try opening one of your own volume or surface files. BTW - you should update MacOS on your machine from 12.6.7 to 12.7 as there are important security fixes in 12.7. - R. On Oct 4, 2023, at 00:53, Clara Massaneda Tuneu <c.massaneda_tuneu(a)blackdog.org.au> wrote:        External Email - Use Caution        Hi, I'm attempting to install and run FreeSurfer, but every time I try to load data, the program unexpectedly quits. I downloaded the license from the email sent by FreeSurfer and followed the instructions of the video tutorial. I've also downloaded and installed the latest version of XQuartz before installing and executing FreeSurfer. When I tried to open FreeView in my terminal and load the image, there was no message in my terminal explaining why the program crashes. The version of FreeSurfer that I'm using is freesurfer-macOS-darwin_x86_64-7.4.1. My device is a MacBook Pro (2016) running version 12.6.7, with a 2 GHz Dual-Core Intel Core i5 processor and 8GB of memory. I've searched the list, and no similar errors have been reported. Does anyone have any thoughts on how to troubleshoot this issue? Thanks for your help.  Clara MT_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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SynthSeg volume labels
by Weerasekera, Akila,PHD 05 Oct '23

05 Oct '23

External Email - Use Caution Hi, Using SynthSeg (Freesurfer dev) with --vol, the .csv does not contain all volume labels, do I need to include anything else in the command? [cid:878677f0-6b6f-4a4d-9c3a-54e1808b22ac] Thank you, Akila Akila Weerasekera, PhD | Postdoctoral Research Fellow Maria Mody lab for Developmental Language and Reading Research Laboratory | Eva Ratai Lab for Clinical Spectroscopy | Garry Nolan Lab (Stanford University) | Harvard Medical School | A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 |Charlestown, MA 02129, USA Mobile: (781) 820 4501 aweerasekera(a)mgh.harvard.edu <mailto:aweerasekera@mgh.harvard.edu> http://secure-web.cisco.com/1pRNH3jpPVm0xhHznjcAnuOO_FSI27YNJi0tVFuibJuCEyI…<http://secure-web.cisco.com/1pRNH3jpPVm0xhHznjcAnuOO_FSI27YNJi0tVFuibJuCEyI…> https://secure-web.cisco.com/158m2Mk7xVvNTOqu1Onlo3GW-mrGUVQUQR1Nxh5mCc2yTr…

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Re: [Freesurfer] segmentThalamicNuclei.sh and Matlab Runtime
by fsbuild 04 Oct '23

04 Oct '23

External Email - Use Caution Try setting DYLD_LIBRARY_PATH to point to the subdirectories containing the Matlab libraries. You could just delete what's there, $ export FREESURFER_HOME=/Applications/freesurfer/7.3.2 $ cd $FREESURFER_HOME $ sudo rm MCRv97 - and re-run fs_Install_mcr, $ cd  bin $ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b .... the script should output the paths to the subdirectories with the libraries to add to DYLD_LIBRARY_PATH at the end of it output.  On the target computer, append the following to your DYLD_LIBRARY_PATH environment variable: /var/folders/yy/abc/install-target/v97/runtime/maci64:/var/folders/yy/abc//install-target/v97/sys/os/maci64:/var/folders/yy/abc/install-target/v97/bin/maci64:/var/folders/abc/install-target/v97/extern/bin/maci64 If MATLAB Runtime is to be used with MATLAB Production Server, you do not need to modify the above environment variable. The paths listed for your machine will be different compared to the above, but just copy and paste what is listed for the entire series of paths into the command, $ export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/var/folders/yy/abc/install-target/v97/runtime/maci64:/var/folders/yy/abc//install-target/v97/sys/os/maci64:/var/folders/yy/abc/install-target/v97/bin/maci64:/var/folders/abc/install-target/v97/extern/bin/maci64 - R. On 10/3/23 21:35, Iglesias Gonzalez, Juan E. (JIGLESIASGONZALEZ@mgh.harvard..edu) wrote:         External Email - Use Caution         Dera Lauren, I am a bit confused: is /Applications/freesurfer/7.3.2/MCRv97 pointing to  /Applications/MATLAB/MATLAB_Runtime/R2019b/MCRv97? Cheers, /Eugenio   -- Juan Eugenio Iglesias http://secure-web.cisco.com/1bqVymEumCTwxGQGbfGgRiZlYNLDyBIOW6zSN5FfiWaLUE4…   From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Lauren Stephens <laurenss(a)stanford.edu> Date: Tuesday, October 3, 2023 at 1:23 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] segmentThalamicNuclei.sh and Matlab Runtime         External Email - Use Caution         Hi FreeSurfers,    I have been attempting to run segmentThalamicNuclei.sh and continue getting the error:    ERROR: cannot find Matlab 2019b runtime in location:       /Applications/freesurfer/7.3.2/MCRv97       It is looking for either:    bin/glnxa64/libmwlaunchermain.so    (Linux 64b) or   bin/maci64/libmwlaunchermain.dylib (Mac 64b)   The hippocampal/amygdala and brainstem modules require the (free) Matlab runtime. You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b. To do so, please run the following command (you might need root permissions):   fs_install_mcr R2019b   For further details, please visit https://secure-web.cisco.com/1ECsrk1Jpk7yzuD5ZaV9DNMKMMh3AzKfgXjXeiMKyBiQtU… Current path setup on our Mac: /Applications/freesurfer/7.3.2/MCRv97   Symbolic link setup on our Mac named MCRv97: /Applications/MATLAB/MATLAB_Runtime/R2019b/MCRv97/bin/maci64/libmwlaunchermain.dylib    However, I have already installed the runtime and have alternatively created a symbolic link with Matlab we already have installed on our Mac.   I have also confirmed the runtime file exists on the machine  ln: MCRv91/MATLAB_R2016b.app: File exists   We are using FreeSurfer version 7.3.2 on an iMac Pro with Ventura 13.6.     Any suggestions for how to get the matlab runtime issue resolved in order to reun the segmentThalamicNuclei.sh code.     Thank you,    Lauren Stephens   Lauren Stephens, MS  Assistant Clinical Research Coordinator  Department of Psychiatry and Behavioral Science  Stanford University School of Medicine   E: laurenss(a)stanford.edu  P: (650)-725-1716   _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1LxpoMnV5h1f2ygJQboSTSQlVwoERVFIH7w5Ps1dKObSS9… The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1RcSTgGvCis3y0KR5iYChzrtturHFp-W2YPdFqxX0vUlq4… <https://secure-web.cisco.com/1o012PTPL0mcyjBi29Y_b3LChA3l48cEePu1IZrA-iRX3q7EM4EByBNYUhLd6I1ZMyZmJOLW3UCfpt6xlVd3kCJHox1NCs6DYMFk1uEk5j71VUyGTr4ujX-HLzY9kA4R1Qb7R8c9yxp9Xo4lpCF-npb6ATBsSMJv7RwHvb0IdSmlrTJaWMSpcxudxsFgHcDfEhXc0tJxE-1f3dPmsV4fvVWGpCTLexoLSiOpXUZIsHJdrMEegyf3wTFykab2qmfji8WK1H5SraTsKi1Huo6b-qRBzjjL3Nf6QogIV9O9QGzDZgL8RUQP4TNRJ3cGF3KwTxn91J-mKGWRf8q1GJVBK0Q/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. 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TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz
by Lauren Stephens 04 Oct '23

04 Oct '23

External Email - Use Caution Hi FreeSurfers, I am trying to troubleshoot an error during TRACULA preprocessing and the issue seems related to the creation of aparc+aseg+thalnuc.nii.gz. The subregion segmentation prior to trac-all -prep was successful and mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz and other Thalamic Nuclei files were generated. In the archives I saw two others have experienced a similar issue without a resolution in the thread. I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6. I have attached the log file, log error, and my configuration file. Any help would be greatly appreciated! Thank you, Lauren Stephens Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behavioral Science Stanford University School of Medicine E: laurenss(a)stanford.edu P: (650)-725-1716

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Free surfer quits unexpectedly
by Clara Massaneda Tuneu 04 Oct '23

04 Oct '23

External Email - Use Caution Hi, I'm attempting to install and run FreeSurfer, but every time I try to load data, the program unexpectedly quits. I downloaded the license from the email sent by FreeSurfer and followed the instructions of the video tutorial. I've also downloaded and installed the latest version of XQuartz before installing and executing FreeSurfer. When I tried to open FreeView in my terminal and load the image, there was no message in my terminal explaining why the program crashes. The version of FreeSurfer that I'm using is freesurfer-macOS-darwin_x86_64-7.4.1. My device is a MacBook Pro (2016) running version 12.6.7, with a 2 GHz Dual-Core Intel Core i5 processor and 8GB of memory. I've searched the list, and no similar errors have been reported. Does anyone have any thoughts on how to troubleshoot this issue? Thanks for your help. Clara MT

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segmentThalamicNuclei.sh and Matlab Runtime
by Lauren Stephens 03 Oct '23

03 Oct '23

External Email - Use Caution Hi FreeSurfers, I have been attempting to run segmentThalamicNuclei.sh and continue getting the error: ERROR: cannot find Matlab 2019b runtime in location: /Applications/freesurfer/7.3.2/MCRv97 It is looking for either: bin/glnxa64/libmwlaunchermain.so (Linux 64b) or bin/maci64/libmwlaunchermain.dylib (Mac 64b) The hippocampal/amygdala and brainstem modules require the (free) Matlab runtime. You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b. To do so, please run the following command (you might need root permissions): fs_install_mcr R2019b For further details, please visit https://secure-web.cisco.com/1dSEOQ7tV8guTp0mVMuBTN-FnaRonB3-Do1A0IPLl4r-ZY… Current path setup on our Mac: /Applications/freesurfer/7.3.2/MCRv97 Symbolic link setup on our Mac named MCRv97: /Applications/MATLAB/MATLAB_Runtime/R2019b/MCRv97/bin/maci64/libmwlaunchermain.dylib However, I have already installed the runtime and have alternatively created a symbolic link with Matlab we already have installed on our Mac. I have also confirmed the runtime file exists on the machine ln: MCRv91/MATLAB_R2016b.app: File exists We are using FreeSurfer version 7.3.2 on an iMac Pro with Ventura 13.6. Any suggestions for how to get the matlab runtime issue resolved in order to reun the segmentThalamicNuclei.sh code. Thank you, Lauren Stephens Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behavioral Science Stanford University School of Medicine E: laurenss(a)stanford.edu P: (650)-725-1716

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Freesurfer October 2023