Freesurfer January 2024

freesurfer@nmr.mgh.harvard.edu

70 participants
111 discussions

Postdoctoral Fellowship in Traumatic Brain Injury and Post-traumatic Epilepsy Neuroimaging
by Gugger, James J 04 Jan '24

04 Jan '24

External Email - Use Caution Postdoctoral Fellowship in Traumatic Brain Injury and Post-traumatic Epilepsy Neuroimaging Description: The Department of Neurology at the University of Pennsylvania Perelman School of Medicine is seeking postdoctoral fellows interested in traumatic brain injury (TBI) and post-traumatic epilepsy (PTE) neuroimaging to conduct research in advanced quantitative analysis of multimodal neuroimaging data. Successful applicants will be aligned with Andrea Schneider MD PhD and James Gugger MD PharmD, to support related research activities including: 1) ARIC Study (Atherosclerosis Risk in Communities) Study: specifically related to a Department of Defense funded ancillary study which aims to investigate associations of TBI with longitudinal changes in neuroimaging biomarkers over a median of 12 years (3 time-points). 2) Transforming Research and Clinical Knowledge in TBI (TRACK-TBI): specifically related to a Department of Defense funded ancillary study which aims to investigate neuroimaging biomarkers of post-traumatic epileptogenesis. In addition to the mentored research projects, the postdoctoral fellow will be expected to present their research at national scientific conferences, prepare and publish manuscripts, pursue additional training/professional development through internal and external courses or workshops, and develop their grant writing skills. The position will be for an initial 1-year with opportunity for renewal for up to 2 additional years. Competitive annual salary (NIH-level minimum will be ensured) and benefits are provided. Additional funding is available for conference travel/presentations. Qualifications: Applicants must have completed a PhD, DrPH, or ScD degree (or a MD, DO, or other equivalent doctoral degree with a research-oriented Master’s degree) in engineering, computer science, neuroscience, biostatistics, epidemiology, or other related quantitative fields. The ideal candidate will have strong computational skills, including proficiency in neuroimaging tools (e.g., FSL, FreeSurfer, Advanced Normalization Tools, etc.) and one or more programming languages (e.g., Python, MATLAB, R, etc.); experience conducting analyses of structural MRI, resting state functional MRI, and diffusion MRI; familiarity with processing and analyzing large datasets leveraging state-of-the-art artificial intelligence and machine learning techniques; as well as proficiency in communication and scientific writing. The ideal candidate has strong organizational skills and the ability to work collaboratively within a diverse team of researchers. Application materials (cover letter, CV, statement of research interests, names and contact information of 1-2 references) should be combined into one PDF and emailed to Dr. Schneider (Andrea.Schneider(a)pennmedicine.upenn.edu<mailto:Andrea.Schneider@pennmedicine.upenn.edu>) and Dr. Gugger (James.Gugger(a)pennmedicine.upenn.edu<mailto:James.Gugger@pennmedicine.upenn.edu>). Review of applications will begin immediately and will continue until the position is filled. Requirement: Must be a U.S. Citizen or Permanent Resident. Contact: Andrea L.C. Schneider, MD, PhD Department of Neurology, Division of Neurocritical Care Department of Biostatistics, Epidemiology, and Informatics University of Pennsylvania Perelman School of Medicine 51 North 39th Street Andrew Mutch Building 416 Philadelphia, Pennsylvania 19104 Phone: 443-827-2352 Fax: 215-662-9858 Email: Andrea.Schneider(a)pennmedicine.upenn.edu<mailto:Andrea.Schneider@pennmedicine.upenn.edu>

1 0

Freeview not showing output
by Shawa, Zeena 04 Jan '24

04 Jan '24

External Email - Use Caution Hello FreeSurfer Developers and Community, Hope your day has been going well and happy new year! I'm attempting to visualise FreeSurfer outputs using freeview, as described on the "Introduction to Freesurfer Output" tutorial, under the "Viewing Volumes with Freeview" section (https://secure-web.cisco.com/1gxz0NYCFZQK8I7yoqBazXhNSxfbtas6xskrsStOsimpxe… ). The viewer launches fine and seems to load everything, but instead of showing any output it simply shows a black screen in the middle (screenshot attached). There is no error outputted in the command line either. The viewer seems to work fine otherwise, and I have completed the Xming X-server setup as described here: https://secure-web.cisco.com/12Wssvth0-cJDruIThEp84njg4hCdzZpcS7NBpfijyPxeJ… . I've searched the archives and GitHub issues and cannot find a similar error. I would appreciate any feedback on how to troubleshoot this issue. Thank you very much for your understanding and help! 1. FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 2. Freeview version: Version 3.0, June 14 2023 build 3. Xming versions: Xming fonts 7.7.0.10, Xming 6.9.0.31 4. Platform: WSL2 Ubuntu 22.04.3 LTS 5. uname -a: Linux LAPTOP-4153LQMG 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 5 21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux 6. specific command: freeview -v \ good_output/mri/T1.mgz \ good_output/mri/wm.mgz \ good_output/mri/brainmask.mgz \ good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f good_output/surf/lh.white:edgecolor=blue \ good_output/surf/lh.pial:edgecolor=red \ good_output/surf/rh.white:edgecolor=blue \ good_output/surf/rh.pial:edgecolor=red Sincerely, Zeena Shawa Zeena Shawa i4Health PhD Student Alan Turing Institute - Roche Community Scholar Research Group UCL Centre for Medical Image Computing [Title: LinkedIn - Description: image of LinkedIn icon]<https://secure-web.cisco.com/1btSHtYkkYjdXpDjgaSZRqJLvx8MmgkH1LViLzSFvV2UaK…> [Title: Twitter - Description: image of Twitter icon] <https://secure-web.cisco.com/10zA_WZOkmHp3Fh1W3Z_sjeqIo7FojuA9hL4g-JNcgF3m3…>

2 3

mri_error_no_clear_message
by Fargol Rezayaraghi 02 Jan '24

02 Jan '24

External Email - Use Caution Hi FreeSurfer Team, I hope this email finds you well. I'm trying to use a T1 image to get the aparc+aseg and wmparc nifti files. I was using this command: recon-all -s Subject1 -i T1.nii - all -notal -check ( I used recon-all -s Subject1 -i T1.nii - all first, and after getting Talairach error, I added -nota -check at the end). I'm getting following messages without clear error number: recon-all -s Subject1 exited with ERRORS at Thu Dec 14 21:18:02 EST 2023 For more details, see the log file /home/developer/Desktop/freesurfer/7.2.0/subjects/Subject1/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1cQznhKx0XPPZTJqsioLqCSeP_2I8A9nJBXfsYwGFwxBXmD… The version of the freesurfer: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b My platform is ubuntu 18_04_06 on Oracle VM VirtualBox I've attached the log file. -- Kind Regards, *Fargol R. Araghi (Rezayaraghi)* Ph.D. Candidate, University of Washington Department of Mechanical Engineering http://secure-web.cisco.com/1etf29AnmyfO7JDA1iwX4HvYcM0WXmMMFv-FG5QUpvlXzXt… <https://secure-web.cisco.com/1OE6aYFeTkmWM7FGsUCe4yHngfS6aQZieqg2uFkxfDu0qu…>

2 2

RA Position Human Brain Mapping Lab
by Winfield, Jalen 02 Jan '24

02 Jan '24

External Email - Use Caution The human intracranial EEG Laboratory at The Feinstein Institutes for Medical Research - Hofstra Northwell School of Medicine in New York is looking for a research assistant with a start date as soon as possible. The successful candidate will help with the lab's research into (1) improving the identification of functional and pathological brain regions in individuals suffering from epilepsy, (2) the neural mechanisms of cognition, and (3) characterization of macro-scale human brain networks. The lab works exclusively with patients being evaluated for epilepsy surgery using methods such as invasive stereo EEG and electrocorticography recordings (iEEG, ECoG), anatomical MRI, fMRI, DTI, and direct electrical brain stimulation. The responsibilities will include assisting with the collection and analysis of the aforementioned data, project management, assistance with grant applications and progress reports, help with analysis of neural and imaging data using existing scripts (Matlab, Python), further development of those scripts (depending on coding and signal processing proficiency), and helping to present lab findings at conferences and in journals. The relative weighting of responsibilities can be adjusted depending on the interest of the applicant. If there is interest, the RA will have a scientific project with dedicated time to work on. Past research assistants have presented their work at clinical and basic research conferences, co-authored publications, and are working on first-author publications. They have gone on to medical schools or PhD programs after spending 1-3 years in the lab. This unique position will expose the successful applicant to basic and clinical neuroscience as well as neurosurgery, neurology, and neuropsychology. The location of the institute allows living either in the suburban neighborhoods of Long Island or in vibrant Brooklyn or Queens. Some employees also commute from Manhattan. It is a great opportunity for recent post-bacs interested in medical school or graduate school in neuroscience/biomedical engineering. ------------- Qualifications ------------- Minimum: - B.A./B.S./B.E. in an appropriate discipline (e.g., neuroscience, psychology, biomedical engineering, computer science, physics) - 2-year commitment - Experience with at least one programming language (MATLAB, R, or Python) Desirable: - Prior experience working with neuroimaging, EEG/MEG, or brain stimulation data - Previous experience working with patients - Previous work in a research laboratory that shows evidence of independent scholarship, problem solving, and motivation For more information about the position please send your CV along with your questions to Dr. Stephan Bickel (sbickel(a)northwell.edu<mailto:sbickel@northwell.edu>). Looking forward to hearing from you! The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

1 0

Longitudinal pipeline with multiple scans at one time point
by Annchen Knodt 02 Jan '24

02 Jan '24

External Email - Use Caution I have a dataset consisting of individuals scanned at two time points 7 years apart. At the first time point, a single MPRAGE scan was collected for each individual; at the second, the same MPRAGE scan was collected, as well as an additional set of 4 shorter MPRAGE scans (collected with the aim of increasing measurement reliability). I’m looking to determine the best way to model the data with the longitudinal pipeline in order to detect reliable change between the two time points (there is test-retest data in a subset at both time points for assessing this). I’m specifically wondering whether it makes sense to compute a base “template” using all 6 scans from a given individual at once (i.e. the matching MPRAGE from tp1 and tp2 + the 4 short MPRAGEs from tp2). My intuition is that doing so would bias the template toward tp2 given that 5/6 images are from that time point, which is undesirable. I am also not sure how the different acquisition types affect things, as the shorter scans do produce systematically [slightly] different measurements. The plan is rely primarily on residual change scores for these analyses, to account for the slight differences in the acquisitions. Any thoughts / suggestions are appreciated – thanks! Annchen Knodt Research Associate Laboratory of NeuroGenetics Duke University

2 2

Freesurfer/Freeview Version Compatibility
by Edwards, Vincent 01 Jan '24

01 Jan '24

External Email - Use Caution Hi, I'm following up on my quick question from this time last week. I have several brains that I sent through recon-all using Freesurfer 7. If I wanted to use Freeview on Freesurfer version 5 to do pial/wm/and control point edits, would I be able to do recon-all through Freesurfer 7? Years ago, someone asked if they could do recon-all in an older version of Freesurfer and edit in a newer GUI. Doug said that was fine. My question is basically the inverse of their problem. I assumed that since Freeview is a GUI, the version used shouldn't have any actual impact on things as long as we returned to version 7 to recon-all. I just want to confirm that my assumption is correct? The pipeline would be: F7 (recon-all), F5 (edit with freeview), F7 (recon-all for pial/wm/cp's) Thanks, Vincent Edwards

2 1

Statistical Characteristics of Segmented Fornix from T1-w MR Images
by Ahsan Ali 01 Jan '24

01 Jan '24

External Email - Use Caution Dear Sir/Madam, I have segmented T1-W MR images from the ADNI database using Freesurfer. From aseg.nii, I have estimated the fornix structure (label number 250). I tried many times to get the characteristics of these structures but couldn't. It would be helpful for me; kindly let me know. File name "fornix.nii" at label 250. Its statistical parameters, such as fractal dimension, volume, mean, etc With Regards Ahsan --------------------------------------------- Ahsan Ali Ph.D Scholar Department of Applied Mechanics and Biomedical Engineering (AMBE) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552

3 4

Case-controls study !
by Martin Juneja 01 Jan '24

01 Jan '24

External Email - Use Caution Hello FreeSurfer experts, In my case-control study, I have a dataset of 5 healthy controls (HCs) and one patient (PAT). I was wondering if there is any way to perform GLM for PAT > HCs on brain morphometry data. When I tried to follow instructions from here: https://secure-web.cisco.com/1og9s8_rd4Lyx1NIwR7d0GRha020qNYi0MbIToxO7mZZ68…, the mri_glm fit command gives me the following error: Class Size and Means of each Continuous Variable 1 HC 5 24.2000 0.6000 2 Tumor 1 50.0000 1.0000 ERROR: Class Tumor has 1 members. With 2 variables and using DODS, you need at least 3 members It seems at-least three subjects are required in the Tumor category - because I have age and sex covariates in my fsgd file. I was wondering if there is any way to still perform the above GLM analysis or any other alternatives available to compare HCs vs one PAT. Thanks!

2 2

mri_cc question
by Dawn Matthews 01 Jan '24

01 Jan '24

External Email - Use Caution Hello Freesurfer team and thank you for your continued responses to questions. My questions pertain to mri_cc, and subsegmentation of the corpus callosum. In prior runs of version 6.0, it seems that aseg outputs the subregions of the corpus callosum. The option for mri_cc also identifies those segments, and (Question 1) I wondered if in version 7.4 how that differs from what aseg normally outputs? In addition, (Question 2) with the -f flag to include the fornix, does this mean that the fornix is incorporated into the five subvolumes, or is the fornix volume calculated separately? (Question 3), For the option to set a different number of segmentations, how does that translate into the five ‘default’ segments (e.g. Anterior, Mid-Anterior, Central, Mid-Posterior, Posterior). Again, thank you for the team’s continued work.

2 1

Freesurfer/Freeview Version Compatibility
by Edwards, Vincent 01 Jan '24

01 Jan '24

External Email - Use Caution Hello, I have several brains that I sent through recon-all using Freesurfer 7. If I wanted to use Freeview on Freesurfer version 5 to do pial/wm/and control point edits, would I be able to do recon-all through Freesurfer 7? I assumed that since Freeview is a GUI, the version used shouldn't have any actual impact on things as long as we returned to version 7 to recon-all. That seemed to be the case when someone asked a similar question (the reverse) <https://secure-web.cisco.com/1T0BQhB8dtRKrnTUmjN8XbkGqwEO9_yqoJso_TElGy705p…> , but that was many years ago so I wanted to confirm. Thanks, Vincent Edwards

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer January 2024