Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30065 discussions

TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz
by Eric Paul Kraybill 12 Oct '23

12 Oct '23

External Email - Use Caution To Whom it may concern, 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 that three 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, and I hope to hear from you soon. Thank you, Eric

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VM image Freesurfer 7.2.0 download
by Tsai, Perry 11 Oct '23

11 Oct '23

External Email - Use Caution Hello, I'm hoping to download the Ubuntu virtual machine disk image of Freesurfer 7.2.0 in order to install onto a new computer. On the website, it appears this link was removed and being updated as of 9/11/23. Is there any timeline on when this download will be available again? Or could I get the previous download file another way? Thanks! *********************EMAIL DISCLAIMER********************* This email and any files transmitted with it may be confidential and are intended solely for the use of the individual or entity to whom they are addressed. If you are not the intended recipient or the individual responsible for delivering the e-mail to the intended recipient, any disclosure, copying, distribution or any action taken or omitted to be taken in reliance on it, is strictly prohibited. If you have received this e-mail in error, please delete it and notify the sender or contact Privacy Office 312.355.5650.

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Hippocampus Segmentation Troubleshoot - Matlab crash
by Mirsol Choi 11 Oct '23

11 Oct '23

External Email - Use Caution Hi there, I am a Master's student who is looking to segment the hippocampus and analyze diffusion data of the segments. I am trying to utilize the segmentation function with this command: segmentHA_T1.sh subj01 But I am met with this error saying that Matlab has crashed. The crash log is attached to this email. I have freesurfer version 7.1.1, running on MacOs 11.7.10. I have followed your website instructions to download Matlab R2014b. Following the installation process of Matlab, I was met with this message: Installing Product: MATLAB Compiler Runtime - Core 8.4 (Oct 08, 2023 11:29:15) Installing Product: MATLAB Compiler Runtime - GPU 8.4 (Oct 08, 2023 11:29:21) Notes: On the target computer, append the following to your DYLD_LIBRARY_PATH environment variable: /var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/bin/maci64: (Oct 08, 2023 11:29:21) Exiting with status 0 (Oct 08, 2023 11:29:21) End - Successful. Finished R2014b installed successfully in /Applications/freesurfer/7.1.1/MCRv84 And so I have appended the path using this code into my bashrc profile: export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/bin/maci64 I am wondering if I can get some help with running the hippocampus segmentation protocol . Thank you so much for your time, I greatly appreciate your support.

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Comparison between groups
by Iara Senem 11 Oct '23

11 Oct '23

External Email - Use Caution Hello! I'm a beginner on FS, hope you can help me. I already ran recon-all and I got aseg and aparc stats into an Excel spreadsheet. Using statistical software (SPSS) I found some differences between controls and patients in some cortical thickness regions. I'd like to know how I can put those differences in a picture. How can I analyze the differences between these groups and get an image on Freeview? Thank you. -- ____________________________________________________ Iara Senem Doutoranda da FMRP-USP Departamento de Neurociências e Ciências do Comportamento da FMRP Neuropsicóloga/Psicóloga - CRP 06/142554 Fone: +55 (16) 98209-1817

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mri_synth functions errors
by K Eswar 10 Oct '23

10 Oct '23

External Email - Use Caution Hello Freesurfer Developers, I am attempting to process mri_synthseg,mri_synthsr,mri_synthstrip and it shows the following error For mri_synthseg and mri_synthsr: Traceback (most recent call last): File "/home/sgbc/freesurfer/python/scripts/mri_synthseg", line 10, in <module> import surfa as sf ModuleNotFoundError: No module named 'surfa' For mri_synthstrip Traceback (most recent call last): File "/home/sgbc/freesurfer/python/scripts/mri_synthstrip", line 5, in <module> import torch ModuleNotFoundError: No module named 'torch' I am using linux operating system_Ubuntu 22.04.2 LTS I have recently installed infant freesurfer and I don't know if the problem is following to it as I expect path might have been changed I tried looking for these errors in the forum, however I did not find the fix. Thank you for your time and consideration Kind regards K Eswar Project scientist Sudha Gopalakrishnan Brain Centre IIT Madras, India

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Re: [Freesurfer] $FREESURFER_HOME/bin not being added to PATH (tcsh)
by fsbuild 10 Oct '23

10 Oct '23

External Email - Use Caution If you add these 2 commands to setup the freesurfer environment, e.g., for csh/tcsh as your default shell, $ setenv FREESURFER_HOME /usr/local/freesurfer/7.4.1-1$ source $FREESURFER_HOME/SetUpFreeSurfer.csh - to your shell initialization file, $HOME/.cshrc, then FREESURFER_HOME, SUBJECTS_DIR, PATH, etc., should automatically set/modified by source'ing SetUpFreeSurfer.csh when you open a new terminal window.   There is no need to subsequently set SUBJECTS_DIR or other freesurfer environment variables in your shell init file (or in the current terminal window session) unless the settings should be different than the defaults.  Most people add those 2 commands to be the last 2 lines in their shell init file. I would check the defaults set in the current shell environment using only those 2 commands above in your shell init file after opening a new terminal window, $ env | sort … and check FREESURFER_HOME, SUBJECTS_DIR, PATH are set … The freeview command should already be found in your path, i.e., you should see … $ which freeview/usr/local/freesurfer/7.4.1-1/bin/freeview - R. On Oct 9, 2023, at 14:56, Edward Zuniga <eazuniga(a)vcu.edu> wrote:        External Email - Use Caution        Hello,I am attempting to install FreeSurfer on a Centos 7 workstation using the tcsh shell. Below are the contents of my .cshrc file. Should $FREESURFER_HOME/bin be automatically added to the PATH? I tried rebooting, and it still is not adding it to the PATH. My environment variables appear to be set correctly  because I see this when opening a new terminal. I also tried modifying the .cshrc file to add the directory to the PATH manually, but it still will not stick after rebooting.-------- freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurfer/7.4.1-1FSFAST_HOME       /usr/local/freesurfer/7.4.1-1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /usr/local/freesurfer/7..4.1-1/subjectsMNI_DIR           /usr/local/freesurfer/7.4.1-1/mniFSL_DIR           /usr/local/FSL/fsl_6_0_7_4[cogdmd@cari6 ~]$ Thanks,Eddie#############################################################umask 002setenv PATH /usr/local/cuda-9.1/bin:$PATHsetenv LD_LIBRARY_PATH /usr/local/cuda-9.1/lib64# auto-inserted by @update.afni.binaries :set path = ( $path  /home/cogdmd/abin  ) setenv R_LIBS ~/R#FSL Setupsetenv FSLDIR /usr/local/FSL/fsl_6_0_7_4setenv PATH ${FSLDIR}/share/fsl/bin:${PATH}source ${FSLDIR}/etc/fslconf/fsl.csh#Freesurfer Setupsetenv FREESURFER_HOME /usr/local/freesurfer/7.4.1-1setenv SUBJECTS_DIR $FREESURFER_HOME/subjectssource $FREESURFER_HOME/SetUpFreeSurfer.cshalias spm12 'matlab -r "addpath /usr/local/SPM/spm12_r7771/spm12; spm fMRI"'alias conn 'matlab -r "addpath /usr/local/SPM/spm12_r7771/spm12; addpath /usr/local/SPM/conn; conn"'setenv PATH /home/cogdmd/anaconda3/bin:$PATHsetenv ANTSPATH /home/cogdmd/ants-2.4.1/binsetenv PATH ${ANTSPATH}:${PATH}setenv PATH /home/cogdmd/.lcmodel:$PATH############################################################-- Edward A. ZunigaSenior Research AnalystVirginia Commonwealth UniversityC. Kenneth and Dianne Wright Center for Clinical and Translational ResearchInstitute for Drug and Alcohol StudiesCollaborative Advanced Research Imaging (CARI) Facility203 East Cary Street, Suite 202Richmond, Virginia 23219Phone: (804) 828-4184Fax: (804) 827-2565eazuniga@vcu.edu_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Job at University of Chicago, neuroimaging for aging/Alzheimer
by Adam Martersteck 10 Oct '23

10 Oct '23

External Email - Use Caution *Apologies for cross-posting listservs* The University of Chicago’s Neurology Department is seeking a data scientist focused on neuroimaging in aging and Alzheimer’s disease. See the full job posting here. <https://secure-web.cisco.com/1yaxNMxhk779aUROY3cicfsnJIUzCUvaeqRL_tkMqoQ7VB…> University of Chicago’s new Healthy Aging & Alzheimer’s Research Care Center is focused on SuperAging, a phenotype of successful aging, and atypical Alzheimer’s disease and related dementia syndromes. Prior experience with Alzheimer’s disease or aging is *not* a requirement. The primary responsibilities of the positions are to use analytical, statistical, and programming skills to help collect, curate, analyze, and interpret biomedical data, including neuroimaging and biomarker derivatives. The candidate will work alongside investigators and clinicians to develop data-driven solutions and answer scientific questions. See the full list of responsibilities in the job posting for more information. Candidates should have some prior experience with neuroimaging software libraries, and Python and/or R. Experience with high-performance cluster shell scripting and schedulers, and machine learning libraries are desirable. Apply through the portal, but feel free to reach out with questions ( martersteck(a)uchicago.edu) *Adam Martersteck, PhD * *(he/him)**Assistant Professor of Neurology* | The University of Chicago, Healthy Aging & Alzheimer's Research Care (HAARC) Center *Address *| 850 East 58th Street | Chicago, IL 60637 *Phone *| 773-795-1683 *Email *| martersteck(a)uchicago.edu

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Re: [Freesurfer] Hippocampus Segmentation Troubleshoot - Matlab crash
by fsbuild 09 Oct '23

09 Oct '23

External Email - Use Caution Please try using the Matlab runtime environment which can be installed directly into the freesurfer tree via a script we provide.  The runtime environment is free and requires no paid for Matlab license (since it does not include the Matlab compiler). For your existing install of freesurfer 7..1.1, the tested version of the Matlab runtime environment to install is R2014b (listed below as the version to use in the bash/zsh commands).  However, if you were to update to the current freesurfer 7.4.1 release, https://secure-web.cisco.com/1EbuUGpusH65Vnhqyq32iw8lhOzpyphG…, then you could use the more recent R2019b Matlab runtime. $ export FREESURFER_HOME=<your install path> $ cd $FREESURFER_HOME/bin $ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2014b    <— change to R2019b if you end up using freesurfer 7.4.1 … answer y to any installer questions … The output from running that script will list what DYLD_LIBRARY_PATH should be set to.   Please make sure you have otherwise removed any references to your previous matlab environment from DYLD_LIBRARY_PATH, PATH, etc.  It might also work to add $FREESURFER_HOME/MCRv97/bin/glnxa64 to DYLD_LIBRARY_PATH but I would first try what the script prints out as the local paths on your machine. - R. On Oct 9, 2023, at 20:21, Mirsol Choi <mirsol(a)ualberta.ca> wrote:        External Email - Use Caution        Hi there,I am a Master's student who is looking to segment the hippocampus and analyze diffusion data of the segments. I am trying to utilize the segmentation function with this command:segmentHA_T1.sh subj01But I am met with this error saying that Matlab has crashed. The crash log is attached to this email. I have freesurfer version 7.1.1, running on MacOs 11.7.10.I have followed your website instructions to download Matlab R2014b.Following the installation process of Matlab, I was met with this message: Installing Product: MATLAB Compiler Runtime - Core 8.4(Oct 08, 2023 11:29:15) Installing Product: MATLAB Compiler Runtime - GPU 8.4(Oct 08, 2023 11:29:21) Notes: On the target computer, append the following to your DYLD_LIBRARY_PATH environment variable:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/bin/maci64:(Oct 08, 2023 11:29:21) Exiting with status 0(Oct 08, 2023 11:29:21) End - Successful.FinishedR2014b installed successfully in /Applications/freesurfer/7.1.1/MCRv84And so I have appended the path using this code into my bashrc profile: export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/bin/maci64I am wondering if I can get some help with running the hippocampus segmentation protocol .Thank you so much for your time, I greatly appreciate your support. <matlab_crash_dump.28607-2>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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$FREESURFER_HOME/bin not being added to PATH (tcsh)
by Edward Zuniga 09 Oct '23

09 Oct '23

External Email - Use Caution Hello, I am attempting to install FreeSurfer on a Centos 7 workstation using the tcsh shell. Below are the contents of my .cshrc file. Should $FREESURFER_HOME/bin be automatically added to the PATH? I tried rebooting, and it still is not adding it to the PATH. My environment variables appear to be set correctly because I see this when opening a new terminal. I also tried modifying the .cshrc file to add the directory to the PATH manually, but it still will not stick after rebooting. -------- freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.4.1-1 FSFAST_HOME /usr/local/freesurfer/7.4.1-1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.4.1-1/subjects MNI_DIR /usr/local/freesurfer/7.4.1-1/mni FSL_DIR /usr/local/FSL/fsl_6_0_7_4 [cogdmd@cari6 ~]$ Thanks, Eddie ############################################################# umask 002 setenv PATH /usr/local/cuda-9.1/bin:$PATH setenv LD_LIBRARY_PATH /usr/local/cuda-9.1/lib64 # auto-inserted by @update.afni.binaries : set path = ( $path /home/cogdmd/abin ) setenv R_LIBS ~/R #FSL Setup setenv FSLDIR /usr/local/FSL/fsl_6_0_7_4 setenv PATH ${FSLDIR}/share/fsl/bin:${PATH} source ${FSLDIR}/etc/fslconf/fsl.csh #Freesurfer Setup setenv FREESURFER_HOME /usr/local/freesurfer/7.4.1-1 setenv SUBJECTS_DIR $FREESURFER_HOME/subjects source $FREESURFER_HOME/SetUpFreeSurfer.csh alias spm12 'matlab -r "addpath /usr/local/SPM/spm12_r7771/spm12; spm fMRI"' alias conn 'matlab -r "addpath /usr/local/SPM/spm12_r7771/spm12; addpath /usr/local/SPM/conn; conn"' setenv PATH /home/cogdmd/anaconda3/bin:$PATH setenv ANTSPATH /home/cogdmd/ants-2.4.1/bin setenv PATH ${ANTSPATH}:${PATH} setenv PATH /home/cogdmd/.lcmodel:$PATH ############################################################ -- Edward A. Zuniga Senior Research Analyst Virginia Commonwealth University C. Kenneth and Dianne Wright Center for Clinical and Translational Research Institute for Drug and Alcohol Studies Collaborative Advanced Research Imaging (CARI) Facility 203 East Cary Street, Suite 202 Richmond, Virginia 23219 Phone: (804) 828-4184 Fax: (804) 827-2565 eazuniga(a)vcu.edu

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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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