Freesurfer August 2021

freesurfer@nmr.mgh.harvard.edu

73 participants
101 discussions

about FreeSurfer QA tools errors
by Xin Qi 13 Aug '21

13 Aug '21

External Email - Use Caution Hi Freesurfer Community Support Team: We would like to use FreeSurfer QA tools. After installing it, I tested it on one subject that finished Freesurfer recon-all processing using the latest FreeSurfer 7.1. but got errors that seem many files are missing in the mri, surf, stat folders created by FreeSurfer. I attach the recon_checker summary log and zipped snaps file for your reference. Looking forward to hearing from you. Thank you very much. Best regards Xin

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Re: [Freesurfer] Announcing FreeSurfer version 7.2
by fsbuild 12 Aug '21

12 Aug '21

External Email - Use Caution Hello Michael, Point taken.  The issue with the exclusion of files under the ./mni directory did not change any source code and no binaries were re-compiled.  The timestamps did change on all the files listed under https://secure-web.cisco.com/1gf9Oci5MYp5_O9OPy-mYs2llFtxC9m8cZj1-QcwGNtoFN…; - R. Michael Krause (krause(a)mpib-berlin.mpg.de) August 12, 2021 at 06:59 External Email - Use Caution Hi, I just found this post and it explains why I'm seeing this: $ ls -lrt freesurfer-linux-centos6_x86_64-7.2.0.tar.gz* -rw-r--r-- 1 krause domain users 4917297770 Jul 15 13:05 freesurfer-linux-centos6_x86_64-7..2.0.tar.gz -rw-r--r-- 1 krause domain users 5012301197 Jul 21 08:13 freesurfer-linux-centos6_x86_64-7.2.0.tar.gz.1 $ md5sum freesurfer-linux-centos6_x86_64-7.2.0.tar.gz* cac0f97a4034c3c234fdbe99707d7d93 freesurfer-linux-centos6_x86_64-7.2.0.tar.gz eae2d09b063794bf2c8ed3e50ee80bd8 freesurfer-linux-centos6_x86_64-7.2.0.tar..gz.1 $ tar tf freesurfer-linux-centos6_x86_64-7.2.0.tar.gz..1 freesurfer/mni/bin/mritotal freesurfer/mni/bin/mritotal $ tar tf freesurfer-linux-centos6_x86_64-7.2.0.tar.gz freesurfer/mni/bin/mritotal tar: freesurfer/mni/bin/mritotal: Not found in archive tar: Exiting with failure status due to previous errors Can I say that, as a sysadmin / package maintainer, I find this a little unfortunate. There is no way for me to know that I had to get a new tar ball, because the version number stayed exactly the same :( It's just that I found this post *after* we stumbled over an issue with the missing MNI directory. best regards Michael fsbuild (fsbuild(a)contbay.com) July 21, 2021 at 14:20         External Email - Use Caution        Hello Kiyotaka, Please try refreshing your copy/install of the Ubuntu 7.2.0 distribution as the packages have been updated to fix the warning below. I think you were using the installer, so you could try the commands below to download and re-install with apt.  (If you were using the tar file then just change the file name in the wget command to be freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz, expand it in the right location and skip the commands with sum, apt remove, apt install). ..... with installer .... $ rm -f  freesurfer_7.2.0_amd64.deb $ wget https://secure-web.cisco.com/1-sNHs519XorwwEeem0CCMvXVsMABHYYE70Coq941BKBnO… $ sum freesurfer_7.2.0_amd64.deb 20191 3199044 $ sudo apt remove freesurfer ..... output deleted ... $ apt install ./freesurfer_7.2.0_amd64.deb ..... output deleted ... ..... check environment ... $ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0 $ source $FREESURFER_HOME/SetUpFreeSurfer..sh ..... the output should have no warnings and you can also check ... $ env | grep MINC MINC_BIN_DIR=/usr/local/freesurfer/7.2.0/mni/bin MINC_LIB_DIR=/usr/local/freesurfer/7.2.0/mni/lib $ which nu_correct /usr/local/freesurfer/7.2.0/mni/bin/nu_correct - R. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1MC4VZX-qXqJcE9riZDC29PvvuojXHgWY2RyPgx5_329PI…

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Researcher Position in Multimodal Imaging and Machine Learning @ University of California, San Francisco (UCSF),
by Tosun, Duygu 12 Aug '21

12 Aug '21

External Email - Use Caution We seek a highly talented and motivated researcher to join UCSF/San Francisco VA to conduct project on the neural mechanisms of neurodegenerative diseases. The overarching aim of the project is to build neural models predicting clinical and pathological disease progression in those who have asymptomatic and symptomatic Alzheimer's pathology. Your duties will be supervising data collection, conducting advanced neuroimaging analyses, including brain connectivity and machine learning, and publishing. There will be ample opportunity to develop your own research questions and focus within this large-scale multidisciplinary project. In addition, you will have the opportunity to supervise students and research assistants who will conduct recruitment and data collection. You will work in a dynamic environment amongst a large group of enthusiastic and high-performing scientists under the umbrella of the Center for Imaging of Neurodegenerative Diseases (CIND) and the Center for Medical Imaging Informatics and Artificial Intelligence led by Dr. Duygu Tosun. Our research center is dedicated to studying the causes and effects of neurodegenerative and psychiatric disorders, using imaging techniques such as MRI and PET. In addition, we work on the development of novel powerful methods for brain MR and new approaches for processing and multivariate statistical analysis of brain imaging. Our research center is equipped with state-of-the art equipment such as a Siemens 3T Skyra and a Siemens 7T. You will be given the opportunity to regularly present your work at international conferences and meetings. Also, in order to develop your own research agenda, we will encourage and support you in applying for competitive career development fellowships towards the end of the project. You should have a PhD or MS degree (or equivalent) and experience in one or more of the following: neuroimaging, neuroscience modeling, statistics, computer science, bioengineering, cognitive neuroscience or related fields. Candidates with a strong background in cognitive neuroscience and experience with advanced neuroimaging data analyses, computational modeling and machine learning, UNIX/ Python/ C++ programming are particularly encouraged to apply. The work environment is casual; however, professional behavior, rapt attention to detail and the ability to meet deadlines are absolute requirements. Candidate must be able to work with a prolific, high-energy scientist with complex schedule needs. The stipend is commensurate with training and experience. The position is available immediately, and applications will be accepted until the position is filled. To apply, please send a brief statement of research interest and goals, any selected reprints, CV, and names and addresses of three references. For additional information or to apply, contact: Duygu Tosun, Ph.D. Department of Radiology and Biomedical Imaging University of California – San Francisco email:duygu.tosun@ucsf.edu https://secure-web.cisco.com/1XpSN5smGMeNE606IR1-tTO083_5YS_GKwstuTjmchngjp… The Center for Imaging of Neurodegenerative Diseases (CIND)<https://secure-web.cisco.com/1XpSN5smGMeNE606IR1-tTO083_5YS_GKwstuTjmchngjp…> The Center for Imaging of Neurodegenerative Diseases (CIND), located at the San Francisco Veterans Affairs Medical Center (SFVAMC) campus of the University of California, San Francisco (UCSF), is a research center dedicated to studying the causes and effects of neurodegenerative and psychiatric disorders, using imaging techniques such as MRI and PET. cind.ucsf.edu Duygu Tosun-Turgut, PhD Director, Medical Imaging Informatics + Artificial Intelligence Associate Professor, UCSF Department of Radiology and Biomedical Imaging https://secure-web.cisco.com/1KrcSneHkpg9MF5yp00LsWYZvThrWtdFDcNijhPgnWPzdf… <https://secure-web.cisco.com/1KrcSneHkpg9MF5yp00LsWYZvThrWtdFDcNijhPgnWPzdf…> University of California, San Francisco Center for Imaging of Neurodegenerative Diseases (CIND) 4150 Clement Street - 114M San Francisco, CA 94121 Phone: (415) 221-4810 ext. 23650 duygu.tosun(a)ucsf.edu

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PhD Position Available @ University of Delaware: Movement Disorders/Parkinson's Disease Research
by Roxana G. Burciu 12 Aug '21

12 Aug '21

External Email - Use Caution The Motor Neuroscience and Neuroimaging Laboratory in the Department of Kinesiology and Applied Physiology at the University of Delaware (https://secure-web.cisco.com/1XTz2R8VijcqZlx4YSp9AX3X5lMJCsbG9XVQU91avZ7TSx… <https://secure-web.cisco.com/1XTz2R8VijcqZlx4YSp9AX3X5lMJCsbG9XVQU91avZ7TSx…>), led by Dr. Roxana Burciu, is seeking motivated and enthusiastic students interested in pursuing a PhD in Neuroscience starting as early as Spring 2022 or Fall 2022. The lab aims to improve our understanding of human neural control of movement and leverage this information to improve motor function, mobility and the quality of life of individuals with movement disorders such as Parkinson’s disease. Students will work in an innovative research program that combines advanced functional and structural brain MRI techniques (task-based and resting state fMRI, arterial spin labelling, diffusion MRI, SWI), behavioral protocols and genetics to understand how the brain and behavior change in people with Parkinson’s disease and those at risk of developing the disease. The lab has access to UD’s Center for Biomedical and Brain Imaging which houses a 3T Siemens Magnetom Prisma whole-body MRI scanner and a 9.4 Bruker Biospec 94/20, designed for pre-clinical MR imaging and MRI research. The lab is also integrated with several other research laboratories studying the neural control of movement in healthy and Parkinson’s disease, which provides a rich scientific and collaborative community. PhD positions are funded through a combination of teaching and research assistantships. Requirements: Have a background in neuroscience, biomedical engineering, kinesiology, psychology, or biomedical sciences. Previous MRI experience is desirable. Have some experience with signal processing, bash, MATLAB or similar programming languages. Be team-minded, flexible with the required tact and sensitivity for working with patients with neurological disorders. Potential applicants should contact Dr. Roxana Burciu at rgburciu(a)udel.edu <mailto:rgburciu@udel.edu> with a brief email expressing their research interests, and a current CV. -- Roxana G. Burciu, Ph.D. | Assistant Professor Department of Kinesiology and Applied Physiology, University of Delaware 347 STAR Tower, 100 Discovery Blvd., Newark DE, 19713 E: rgburciu(a)udel.edu <mailto:rgburciu@udel.edu> | T: (302)-831-3066 | F: (302)-831-8813 Motor Neuroscience and Neuroimaging Lab: https://secure-web.cisco.com/1XTz2R8VijcqZlx4YSp9AX3X5lMJCsbG9XVQU91avZ7TSx… <https://secure-web.cisco.com/1XTz2R8VijcqZlx4YSp9AX3X5lMJCsbG9XVQU91avZ7TSx…>

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[Quick Question] Freeview Update
by Boa Sorte Silva, Narlon 12 Aug '21

12 Aug '21

External Email - Use Caution Dear FreeSurfer team, We have half of our sample edited in Freeview V2, we wanted to updated to the latest version of Freeview, would it be a problem if the other half were to be edited in this newest version? I understand reprocessing of data should be done in the same version/machine, however I was curious about editing. Thanks, Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSFHR/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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Subject with extremely large ventricles
by Shane Schofield 12 Aug '21

12 Aug '21

External Email - Use Caution Hi Freesurfer Experts, Is there anything that could be done to improve the surface definitions for this particular subject (attached)? The pial and white matter boundaries in the cortex are generally accurate though. Thank you. Best Wishes,Shane

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error running samseg on cluster
by Ritobrato Datta 12 Aug '21

12 Aug '21

External Email - Use Caution Hi All, I am trying to run samseg as follows on a cluster and am getting a message that I need to install tensorflow (which is already installed). Please see below. Please advise how to fix this. Many thanks Rito ------------------------------------------------------------- run_samseg --input t12t2.nii.gz t2_brain.nii.gz --lesion --lesion-mask-pattern 0 1 --save-posteriors --output t2_lesions error: This tool requires tensorflow, but fspython does not ship with tensorflow by default. You (or a sys admin) can install the CPU version via:fspython -m pip install tensorflow==1.13.1 fspython -m pip install tensorflow==1.13.1 Requirement already satisfied: tensorflow==1.13.1 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (1.13.1) Requirement already satisfied: protobuf>=3.6.1 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (3.17.3) Requirement already satisfied: keras-applications>=1.0.6 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.0.8) Requirement already satisfied: absl-py>=0.1.6 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (0.13.0) Requirement already satisfied: six>=1.10.0 in /home/rito/software/freesurfer7/python/packages (from tensorflow==1.13.1) (1.14.0) Requirement already satisfied: grpcio>=1.8.6 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.39.0) Requirement already satisfied: termcolor>=1.1.0 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.1.0) Requirement already satisfied: astor>=0.6.0 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (0.8.1) Requirement already satisfied: gast>=0.2.0 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (0.5.2) Requirement already satisfied: numpy>=1.13.3 in /home/rito/software/freesurfer7/python/packages (from tensorflow==1.13.1) (1.18.4) Requirement already satisfied: keras-preprocessing>=1.0.5 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.1.2) Requirement already satisfied: wheel>=0.26 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (0.37.0) Requirement already satisfied: tensorboard<1.14.0,>=1.13.0 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.13.1) Requirement already satisfied: tensorflow-estimator<1.14.0rc0,>=1.13.0 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.13.0) Requirement already satisfied: h5py in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from keras-applications>=1.0.6->tensorflow==1.13.1) (3.1.0) Requirement already satisfied: markdown>=2.6.8 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (3.3.4) Requirement already satisfied: werkzeug>=0.11.15 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (2.0.1) Requirement already satisfied: mock>=2.0.0 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow-estimator<1.14.0rc0,>=1.13.0->tensorflow==1.13.1) (4.0.3) Requirement already satisfied: cached-property; python_version < "3.8" in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from h5py->keras-applications>=1.0.6->tensorflow==1.13.1) (1.5.2) Requirement already satisfied: importlib-metadata; python_version < "3.8" in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from markdown>=2.6.8->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (4.6.3) Requirement already satisfied: dataclasses; python_version < "3.7" in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from werkzeug>=0.11.15->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (0.8) Requirement already satisfied: zipp>=0.5 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from importlib-metadata; python_version < "3.8"->markdown>=2.6.8->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (3.5.0) Requirement already satisfied: typing-extensions>=3.6.4; python_version < "3.8" in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from importlib-metadata; python_version < "3.8"->markdown>=2.6.8->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (3.10.0.0) You are using pip version 18.1, however version 21.2.3 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

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FreeSurfer QA TOOLS errors
by Xin Qi 12 Aug '21

12 Aug '21

External Email - Use Caution Hello FreeSurfer Developers: We would like to use FreeSurfer QA TOOLS. After installing it, I tested it on one subject that finished Freesurfer recon-all processing using the latest FreeSurfer 7.1. but got errors that seem many files are missing in the mri, surf, stat folders created by FreeSurfer 7.1, which are requested by FreeSurfer QA TOOLS I attach the recon_checker summary log and zipped snaps file for your reference. *1) FreeSurfer version: * freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 *2) Platform: *Ubuntu 18.04.5 LTS (Bionic Beaver) *3) uname -a:* Linux ip-10-111-250-7 5.4.0-1039-aws #41~18.04.1-Ubuntu SMP Fri Feb 26 11:20:14 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux *4). recon_checker.ALL.summary.log:* see attached file with zipped snaps folder contains snap shoots Looking forward to hearing from you. Thank you very much. Best regards Xin

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Re: [Freesurfer] Announcing FreeSurfer version 7.2
by fsbuild 12 Aug '21

12 Aug '21

External Email - Use Caution Hello Kiyotaka, Please try refreshing your copy/install of the Ubuntu 7.2.0 distribution as the packages have been updated to fix the warning below. I think you were using the installer, so you could try the commands below to download and re-install with apt.  (If you were using the tar file then just change the file name in the wget command to be freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz, expand it in the right location and skip the commands with sum, apt remove, apt install). .... with installer ... $ rm -f  freesurfer_7.2.0_amd64.deb $ wget https://secure-web.cisco.com/1i8WchnZn-ZDMrXexp7WlIVIxgdWjuz06xq1yUvfYcAZHM… $ sum freesurfer_7.2.0_amd64.deb 20191 3199044 $ sudo apt remove freesurfer .... output deleted .... $ apt install ./freesurfer_7.2.0_amd64.deb .... output deleted ... .... check environment ... $ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh .... the output should have no warnings and you can also check ... $ env | grep MINC MINC_BIN_DIR=/usr/local/freesurfer/7.2.0/mni/bin MINC_LIB_DIR=/usr/local/freesurfer/7.2.0/mni/lib $ which nu_correct /usr/local/freesurfer/7.2.0/mni/bin/nu_correct - R. -------- freesurfer-linux-ubuntu18_x86_64-7.2.0-20210714-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurfer/7.2.0FSFAST_HOME       /usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /home/username/freesurfer/7.2.0/subjectsWARNING: MINC_BIN_DIR not defined.         'nu_correct' and other MINC tools         are used by some Freesurfer utilities.         Set NO_MINC to suppress this warning.WARNING: MINC_LIB_DIR not defined.         Some Freesurfer utilities rely on the         MINC toolkit libraries.         Set NO_MINC to suppress this warning.FSL_DIR           /usr/local/fsl =====

3 2

fsaverage file download
by Shruthi Srinivasan 10 Aug '21

10 Aug '21

2 1

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Freesurfer August 2021