Freesurfer October 2021

freesurfer@nmr.mgh.harvard.edu

81 participants
113 discussions

FW: [All] Fwd: Research Computing Position in Kilachand
by Fischl, Bruce 20 Oct '21

20 Oct '21

FYI ---------- Forwarded message --------- From: Stern, Chantal E <chantal(a)bu.edu<mailto:chantal@bu.edu>> Date: Thu, Oct 14, 2021 at 6:11 PM Subject: Re: Research Computing Position in Kilachand Hi Everyone, We are still looking to fill this position. Please post or send to anyone who might be interested! Best, Chantal Chantal E. Stern, D.Phil. Director, Cognitive Neuroimaging Center Center for Systems Neuroscience Center for Memory and Brain Dept. of Psychological and Brain Sciences Kilachand Center for Integrated Life Science and Engineering 610 Commonwealth Ave, 903 Boston University Chantal(a)bu.edu<mailto:Chantal@bu.edu> -- RESEARCH COMPUTING APPLICATIONS AND DATA SPECIALIST III, IS&T Research Computing MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://bu.silkroad.com/epostings/index.cfm?fuseaction=app.jobinfo&id=23&jo…<https://secure-web.cisco.com/1WEP_6DaE8z0K5agD50NSi_Qgb8rD-1QM8_mV53ohSLnky…> Tracking Code 0079 Job Description The Research Computing Applications & Data Specialist III will lead the technical aspects of Research Computing services and service components related to consulting, training, scientific application package support, and the development, porting, and optimization of research computing software focused on computational neuroscience, neuroimaging, neuro-engineering, and synthetic biology. Serve as the primary support contact for faculty and graduate students working in the above areas particularly those located in the Center for Integrated Life Sciences and Engineering (CILSE) on complex projects and issues which require in-depth knowledge of the multiple technical areas, as well as the core computational research tools which they utilize. Work directly with faculty and other academic stakeholders to assess needs and recommend solutions as a representative of the Research Computing team. Coordinate with Desktop Support and other IS&T groups to ensure the most efficient and effective solutions to researcher computing needs. Required Skills • Graduate training in Engineering, Bioinformatics, Neuroscience, or related training field. or an equivalent combination of education and experience required. • 5-8 years of relative work experience preferred. • Extensive knowledge of neuroimaging and computational neuroscience software packages such as Freesurfer, FSL, SPM, etc.) • Experience with fMRI analysis and constructing and optimizing analysis pipelines. • Fluency in multiple programming languages (including MATLAB, Python, R) and the ability to quickly learn new programming languages and tools as required • Experience with command-line development tools in a Linux environment is desired - • Experience with the architecture, design, and implementation of the software and hardware computational frameworks for neuroimaging, including familiarity with XNAT/ DICOM file processing and NiFTI-1 file processing • Extensive experience with supporting life sciences research, including neuroscience and neuroimaging research • Strong analytical skills are required with an ability to manage multiple projects and deliverables • Excellent communication and presentation skills, the ability to convey technical information in a clear and thorough manner We are an equal opportunity employer and all qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability status, protected veteran status, or any other characteristic protected by law. We are a VEVRAA Federal Contractor. Job Location BOSTON, United States Position Type Full-Time/Regular Salary Grade Grade 50

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SynthSR
by Castro Leal, Gonzalo 18 Oct '21

18 Oct '21

External Email - Use Caution Dear Freesrufer Developer, I have noticed that the ubuntu edition has not been updated since 05/10 (dd/mm) and the issue with the synthsr tool is later to that. However, there is a python script named mri_SynthSR that on the centos version is synthsr. My doubt in the end is if synthsr in centos equals mri_SynthSR in ubuntu , and if the ubuntu version works fine or needs to be updated. Many thanks, Gonzalo.

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How to obtain parahippocampus segmentations?
by Jingyi Wang 18 Oct '21

18 Oct '21

External Email - Use Caution Dear Freesurfer experts, I am trying to obtain parahippocampus segmentations from the "?h.aparc.a2009s.annot" file. However, after running the "mri_annotation2label" commands, I cannot find any label that belongs to the parahippocampus segmentation. Any suggestions? Thank you in advance. Jingyi

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Research Specialist - UW- Madison, WI (Center for Healthy Minds)
by CHM Recruiting 18 Oct '21

18 Oct '21

External Email - Use Caution Research Specialist, UW- Madison, WI, Center for Healthy Minds Are you interested in how emotional and brain processes are related to life experiences, cognition, health, and well-being? The Research Specialist will be responsible for scientific integrity of data collection, data cleaning, and data processing for the Emotion and Wellness Study, led by Dr. Stacey Schaefer, at the University of Wisconsin-Madison's Center for Healthy Minds. Data collection includes in-person study visits, working with a participant one-on-one collecting a variety of questionnaires, cognitive/behavioral tasks, biomarkers (e.g. saliva and dried blood spots), psychophysiology (e.g. facial electromyography, heartrate, respiration and skin conductance), and neuroimaging (e.g. functional and structural MRI). This position requires good people and communication skills, and flexibility to work with people from a wide age-range and different backgrounds. Opportunities exist to learn a variety of data processing techniques and skills. Please go to https://secure-web.cisco.com/1Zf73pYY8VMjVLZS11Db1pOKksXzIz1b_4QF0Nrxlz5im_… to view the complete job posting and apply online. Deadline to apply is November 2, 2021. UW-Madison is an affirmative action/equal employment employer and we encourage women, minorities, veterans, and people with disabilities to apply.

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Topological error on recon after manual edits
by M Pope 18 Oct '21

18 Oct '21

External Email - Use Caution Hi all, I ran recon-all successsfully on a subject. I then did some manual edits on both the brainmask (removal of dura) and wm and then ran recon again for the edits. This usually works fine, however for one subject the recon (after edits) fails because of time limit on my process. It gets stuck on the fix toplogical errors stage, as there is a defect with 36000+ vertices included. I looked at the lh.inflated.nofix and lh.orig.nofix and indeed you can see there is a lot of dura/skull being included in the surface on the lh. However, recon did work just fine the first time where these did happen, and the final surfaces look fine (the manual edits I did were few!) Gcut also does not work because it removed too much of the temporal areas and the cerebellum. Are there any suggestions on how to fix this without having to go in and manually remove all the dura (it is a lot!). I attach the recon.all log so you can see how the first recon ran (without errors) and then after edits where it fails. Could I perhaps use the -nofix flag? Thanks, Marianna

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mri_surf2vol with inflated surfaces
by Nicolas Munera Garzon 18 Oct '21

18 Oct '21

External Email - Use Caution Greetings freesurfuer community, I've been working on a research project for which I need to simulate different levels of inflation for a given brain MRI, to achieve so I have tried the following so far: 1. To run recon-all for a test subject 2. To run mris_inflate over pial surfaces (as that's the structure I need for my simulation) 3. To try to get back to a .nifti file by using mri_surf2vol. However I have been unsuccessful with this step as the required --ribbon parameter refers to ribbon.mgz which is a binary mask of segmented tissue. My question: is there a way for me to generate a ribbon.mgz with the inflated brain, or does anyone know how to get an inflated version of the brain that I can use as an actual volume / image (.nifti, .mgz...)? Thanks in advance! -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web http://secure-web.cisco.com/12-1T4t5I3WmZta2EqCjvwIWHtQeGJkmeNAZoRBbnrgdUpK… <http://secure-web.cisco.com/1ggE-ylwUekBVUwUxvozHFy8vy00YXExkO6K6A3ePYD9meH…>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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ACPC alignment before processing
by Zhengchen Cai 18 Oct '21

18 Oct '21

External Email - Use Caution Hello FreeSurfer Developers, I wonder if we have a function that could automatically align T1w to ACPC before running recon-all? Or if we have an option in recon-all that could do this ACPC alignment automatically? I noticed there are such ways after running freesurfer by applying the transformation matrix, but I guess it will be less convenient than pre-alignment since we don't bother to transform all the output. Especially if we use freesurfer with other tools like fMRIPrep, all functional images will also be registered to ACPC aligned T1w. I ask this since sometimes the T1w is tilted and not desirable for visualization purposes. Thanks a lot. Best regards, Zhengchen

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Different pixel spacing for scans in the same cohort
by Castro Leal, Gonzalo 18 Oct '21

18 Oct '21

External Email - Use Caution Dear Freesurfer, I was wonderign wether processing scans and comparing their stats, e.g. cortical thickness and area, could be not recommended if the pixel spacing across all the scans was different, i.e. the range is between .9375x.9375x1.2 and 1.3542x1.3542x1.2. Many thanks, Gonzalo.

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MEMPRAGE protocol
by nicola spotorno 18 Oct '21

18 Oct '21

External Email - Use Caution Dear all, I read on the FAQ that MGH would kindly share an optimized MEMPRAGE. I was wondering how/how should I get in touch to discuss about this option. All the best, Nicola

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Job Posting - Center for Healthy Minds
by CHM Recruiting 18 Oct '21

18 Oct '21

External Email - Use Caution Hello, Would you please list the attached on the Freesurfer (listserv): Research Specialist - UW Madison, WI - Center for Healthy Minds. Thank you, Lisa Wesley Human Resources Generalist Center for Healthy Minds lawesley(a)wisc.edu

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Freesurfer October 2021