Freesurfer April 2021

freesurfer@nmr.mgh.harvard.edu

104 participants
144 discussions

Question about volume matrix in hippocampus
by Wei Shao 22 Apr '21

22 Apr '21

External Email - Use Caution Hi, Freesurfer experts. I have used "quantifyHAsubregions.sh hippoSf" to gather the volume information from the hippocampus. A quick question about the volume matrix, would you tell me which label system ("HBT" "FS60" or "CA") this code used to extract the volume information? or there is no difference? Thanks Best, Wei

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Hippocampal Subfields
by Jindal, Saurabh 22 Apr '21

22 Apr '21

External Email - Use Caution Hi experts, I am focusing on hippocampus for my work using subfield analysis on freesurfer 7.1. Is there is way to run the container only for subfields or do we have to run recon_all on the subject first always? Thanks. Saurabh Postdoc Research Fellow ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Postdoctoral Researcher Position in Adolescent and Infant Neuroimaging
by Jeffrey Spielberg 21 Apr '21

21 Apr '21

External Email - Use Caution *Attachment and Biobehavioral Catch-up Lab* *University of Delaware, Newark, DE* *Postdoctoral Researcher Position in Adolescent and Infant Neuroimaging* We invite applications for a postdoctoral position within a highly interdisciplinary lab at the University of Delaware investigating the short- and long-term effects of an evidence-based parenting program on brain development. The researcher will play a role in analyzing and publishing data from our NIH-funded randomized clinical trial that uses functional and structural MRI to investigate how enhanced early care shapes the developing connectome. The researcher will join an inter-disciplinary group of researchers with expertise in intervention science, genetics, psychophysiology (autonomic nervous system regulation and cortisol regulation) and neuroimaging (EEG and MRI). The candidate will be supervised by Dr. Mary Dozier, Dr. Nim Tottenham and Dr. Jeffrey Spielberg. REQUIREMENTS: - Ph.D. in neuroscience, psychology, clinical or developmental science or related disciplines - Experience processing and analyzing structural and functional MRI data ADDITIONAL HIGHLY DESIRED QUALIFICATIONS: - Proficiency in MATLAB or R and/or computer programming (e.g., bash scripting) - Previous publications using MRI data - Interest in neuroimaging of infants and adolescents - Strong interpersonal skills - Collaborative team member EXPECTED RESPONSIBILITIES: - Analyze human MRI data using various software tools (in particular FSL, Freesurfer) - Prepare manuscripts for publication - Collaborate with graduate students and assist in their training in data processing and analysis - Assist with data collection and organization of participant data - Participate in grant and laboratory management How to apply: Please email your CV, a brief statement of research experience and interests, and a list of three references with contact information to Dr. Mary Dozier (mdozier(a)udel.edu) For more information on the lab’s work, see: http://secure-web.cisco.com/1SxgDGinFmIeQuPoN8yeUtMVtl17FMqlcTwlK7zPrVkLAYP… -- Jeffrey M. Spielberg, Ph.D. Assistant Professor, Clinical Science Department of Psychological and Brain Sciences University of Delaware Newark, DE 19716 Lab: Suite 405 Wolf Hall Email: jmsp(a)udel.edu Website: http://secure-web.cisco.com/17lxMc4SBgA-riBFZdmUtiIpQotTNwUrJVED9Lk8uLUOtrg…

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mri_recon-all error : number of vertices does not match surface
by 林鈺庭 21 Apr '21

21 Apr '21

External Email - Use Caution Dear FreeSurfer Developers: We analyzed MRI T1 image data on freesurfer and encountered some difficulty, could you help us with this? The recon-all.log file is already attached in this email in case you need it. We thank you in advance. - FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c - program versions used:$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ Best regards, Josephine

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error installing tensorflow
by AJ 21 Apr '21

21 Apr '21

External Email - Use Caution Hi, I am having trouble installing: fspython -m pip install tensorflow==1.13.1 Not sure what the issue is. Any help would be greatly appreciated. best AJ Error message while installing: dyld: lazy symbol binding failed: Symbol not found: _utimensat Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3 Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: _utimensat Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3 Expected in: /usr/lib/libSystem.B.dylib

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Freeview - manjaro
by Vishnu S 21 Apr '21

21 Apr '21

External Email - Use Caution I'm getting a repeated error with libjpeg.so.62. is there any known fix?

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MGH/Harvard: Postdoc in brainstem diffusion and PET imaging in aging/dementia
by Jacobs, H (NP) 21 Apr '21

21 Apr '21

External Email - Use Caution Postdoc Position in the Department of Radiology, Massachusetts General Hospital / Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in Boston, Massachusetts, has an opening for highly qualified individuals at the post-doctoral level to work with Dr. Heidi Jacobs. The Jacobs lab is part of the Gordon Center for Medical Imaging at MGH and focused on improving the early detection and early treatment of Alzheimer’s disease. The lab focuses on the neuromodulatory subcortical nuclei, in particular the locus coeruleus, using a variety of approaches, including 7T MRI, PET imaging, pupil measurements, physiological recording, blood-based markers and cognitive assessments. This postdoc will be involved in a new NIA-funded project working on new methods in PET and diffusion imaging to examine tau propagation in aging and Alzheimer’s disease. Our team and this project is embedded within the Harvard Aging Brain Study (HABS). Ideal start date is around July/August 2021. Most of the work in this project will be performed at the Athinoula A. Martinos Center for Biomedical Imaging, Charlestown Navy Yard. The candidate will be part of ongoing collaborations and be able to work in a stimulating and inspiring environment. The Department of Radiology at MGH is equipped with the first mobile PET/CT, the first brain PET/MRI, the first whole-body PET/MRI in the USA and several MRI scanners, including two 7T ultra-high-field scanner. It is equipped with a large-scale shared memory computing facility for parametric image analysis, tomographic reconstruction, Monte Carlo simulation, and other computationally intensive research applications. Our research group values open communication, motivation, optimism, mutual respect, teamwork, and innovative thinking. Dr. Jacobs is highly committed to individualized mentoring to help trainees achieve the most out of their postdoctoral candidature and to move forward in their career. At a minimum, the training environment will include professional development, one-on-one meetings, group lab meetings, frequent seminars and journal clubs, opportunities to present their work at national and international scientific conferences (i.e. Human Amyloid Imaging, Alzheimer’s Association International Conference, OHBM), and manuscript preparation for publication in high impact journals. In addition, Dr. Jacobs has a strong funding record and will strongly encourage and provide mentorship in grant applications. Requirements: Candidates should have a Ph.D. in Cognitive Neuroscience, Computational Neuroscience, Medical Physics, Computer Science, Biomedical Engineering or related disciplines. Strong analytical, quantitative and programming skills as well as expertise in diffusion imaging are essential. Prior experience in PET is advantageous. The candidate should be highly motivated, a strong communicator, possess internal drive to learn independently, but also be comfortable with working as part of a larger collaborative team. A real necessity is a passion for science, strong scientific writing and organizational skills, and a positive attitude. Experience in Alzheimer’s disease dementia or aging would be beneficial. MGH & HMS are equal-opportunity, affirmative action employers. Women and minority candidates are encouraged to apply. [cid:image001.png@01D736D8.2A770D00]Apply: The successful candidate will have joint appointments at MGH and HMS. If interested, please send your CV, letter describing interests, background, major achievements, skills, goals and contact information for three professional references. Please send application materials to Dr. Heidi Jacobs, Assistant Professor of Radiology, at hjacobs(a)mgh.harvard.edu<mailto:hjacobs@mgh.harvard.edu> Or go to: https://secure-web.cisco.com/1CVgdVGKSr9D3ATbyst3zG4_gz-77rYgEGs9ReQqA4IVg9… , job nr 3153522

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Re: [Freesurfer] Hipppocampal segmentation on freesurfer
by Iglesias Gonzalez, Juan E. 21 Apr '21

21 Apr '21

Dear Saurabh, Is this recon-all (aseg.mgz), or the hippocampal subfield module? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Jindal, Saurabh" <jindals(a)wustl.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, April 20, 2021 at 11:30 To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hipppocampal segmentation on freesurfer External Email - Use Caution External Email - Use Caution Hi experts, I am working on freesurfer 7.1 now and my ROI is hippocampus, but it seems that there is some non-hippocampal inclusion in the form of choroid plexus and adjacent peri-ventricular white matter. Do we have a standard cutoff criterion for hippocampal inclusion? Like how many voxels for how many slices is okay to let it pass? Saurabh ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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question about mapping fsaverage surface atlas to subject's native volume space
by Ren, Xueying 21 Apr '21

21 Apr '21

External Email - Use Caution Dear experts, I am trying to convert an atlas which is in fsaverage surface space to each subject's native volume space. However, the alignment seems off (e.g., in the parietal lobe, see attached screenshot). I am not sure where the problem is. Here is the code that I used: tkregister2 --mov ${subj_dir}/${subj_id}/mri/rawavg.mgz --targ ${subj_dir}/${subj_id}/mri/orig.mgz --reg register.native.dat --noedit --regheader mri_surf2vol --surfval lh.Wang2015.mgz --hemi lh --subject fsaverage --fillribbon --reg register.native.dat --template ${subj_dir}/${subj_id}/mri/001.mgz --o lh.Wang2015.native.nii.gz Any help would be highly appreciated! Thank you! Caroline

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docker pull freesurfer: manifest error
by Chr. Roßmanith 20 Apr '21

20 Apr '21

External Email - Use Caution Hi, I'd like to use FS 7 in a docker container. When pulling freesurfer I get the following error message: docker pull freesurfer/freesurfer Using default tag: latest Error response from daemon: manifest for freesurfer/freesurfer:latest not found: manifest unknown: manifest unknown Any hint what I'm doing wrong? Regards, Christina Roßmanith

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Freesurfer April 2021