Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

Re: [Freesurfer] VM developer password
by fsbuild 08 Feb '22

08 Feb '22

External Email - Use Caution Sending to your email shortly. - R. On Feb 8, 2022, at 13:11, Dale Pike <dale.pike(a)gmail.com> wrote:        External Email - Use Caution        I understand that this is where I am to request a password to the Ubuntu VM image for the developer account? Please advise.Thanks,Dale_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

VM developer password
by Dale Pike 08 Feb '22

08 Feb '22

External Email - Use Caution I understand that this is where I am to request a password to the Ubuntu VM image for the developer account? Please advise. Thanks, Dale

1 0

FW: Survey testing experimental setup
by Lepauvre, Alex 08 Feb '22

08 Feb '22

External Email - Use Caution Dear Freesurfer community, Our survey to regarding common practices to test experimental setup will be over soon. If you haven't had time to fill it out just yet, here is the link again. We are looking forward to your responses :) Thanks in advance for your help, Kind regards, Alex From: Lepauvre, Alex Sent: Monday, 31 January 2022 09:11 To: 'freesurfer(a)nmr.mgh.harvard.edu' <freesurfer(a)nmr.mgh.harvard.edu> Subject: Survey testing experimental setup Dear Freesurfer community, Have you ever wondered what is the impact that the experimental setup might have on reported results in neuroscience and psychology? If yes, you are not alone! We have created a survey to better understand and identify common practices used in the field to test experimental code and experimental hardware. This survey is addressed to anyone having undertaken the programming, implementation and testing of a neuroscientific or psychophysical experiment at some point in their careers. The responses to the survey are anonymized and the data will be presented as aggregates. We aim to collect responses from a wide variety of researchers, hopefully at different career stages. Feel free to share the link with as many of your peers as possible. The survey will take no more than 5 mins to be completed. By clicking on this link, you will proceed to the survey: https://secure-web.cisco.com/1fKDJuWL3IFUkiyyHuSdPDvH7BPDhY3S5gKmEnllfEETXM… Thanks in advance for your help! Kind regards, Alex & Rony Alex Lepauvre, Max Planck institute for empirical aesthetics, Frankfurt, Germany Rony Hirschhorn Tel-Aviv University, Tel Aviv, Israel

1 0

Using -bigventricles for infant segmentation
by Fateme Sadat Haghpanah 07 Feb '22

07 Feb '22

External Email - Use Caution Dear FreeSurfer Developers, I am trying to use the InfantFS segmentation pipeline for segmenting images with Ventriculomegaly. I have looked up the archive and found out the -bigventricles. I have tried the following commands but it did not work. Can you help me to figure out how I can segment these images with infantFS? infant_recon_all -bigventricles --newborn --s ${SUBJ} —> ERROR: Flag -bigventricles unrecognized Regards, Fateme

2 2

PhD position in Cognitive Neuroscience
by Nicolas Langer 07 Feb '22

07 Feb '22

External Email - Use Caution PhD position in Cognitive Neuroscience Department: Department of Psychology at the University of Zurich (Switzerland), Methods of Plasticity Research (http://secure-web.cisco.com/1yrXnmcLak8VcmE09mDHZoci-sk4X3q07igz895-SUBVrvp… <http://secure-web.cisco.com/1yrXnmcLak8VcmE09mDHZoci-sk4X3q07igz895-SUBVrvp…>) Position: PhD student (salary 54’000 USD/year) Description of UZH unit: Our lab develops novel methodological approaches to study variations in cognitive performance across the lifespan and along the continuum from healthy to pathological functioning. Specifically, we investigate the potential for plasticity, mechanisms for stabilization and compensation across the lifespan. For this, we acquire and analyze multimodal data sets, such as structural MRI, diffusion weighted data (DWI), simultaneous EEG and eye-tracking as well as behavioral data. From these rich data sets, we extract multivariate parameters and apply state-of-the-art methods, such as machine learning, functional network modelling, and longitudinal analyses. Responsibilities: The successful candidate will work on the Synapsis-foundation funded research project “Real-life activity tracking as pre-screening tool for early stages of Alzheimer disease”. The aim of the project is to investigate whether real-life activity measures, derived from wearable technology (e.g. GPS and accelerometer data), are sensitive to identify early stages of Alzheimer’s disease. Further, we aim to provide evidence that these real-life activity measures are associated with current AD biomarkers (i.e. high Amyloid level and brain atrophy). The student will be expected to disseminate study results in peer reviewed journals, and to supervise Master’s students. The candidate will work in the team of Prof. Nicolas Langer, who is also part of the Neuroscience Center Zurich (ZNZ) (https://secure-web.cisco.com/1j9dVWlEovAAe9t5FR6nKcRvk_0Yl721sHAUBF-hXb_iJz… <https://secure-web.cisco.com/1j9dVWlEovAAe9t5FR6nKcRvk_0Yl721sHAUBF-hXb_iJz…>), which offers a renowned international PhD programme in Neuroscience. The candidate will work closely with the Institute for Regenerative Medicine (https://secure-web.cisco.com/1c97BxJICcB3NTZIZFQKFhpVHVc-8EJh72iy6rEy22EbOj… <https://secure-web.cisco.com/1c97BxJICcB3NTZIZFQKFhpVHVc-8EJh72iy6rEy22EbOj…>), Geographic Information Systems (https://secure-web.cisco.com/10BeiM-zzcFs3UtSRm8gQk7oMwijYSyO4gQhISpbG9k_m6… <https://secure-web.cisco.com/10BeiM-zzcFs3UtSRm8gQk7oMwijYSyO4gQhISpbG9k_m6…>), University Research Priority Programme from the University of Zurich “Dynamics of Healthy Aging” (https://secure-web.cisco.com/1ES7m6_j-xtuKVPJ2bSeckrMa9dywupWgezD1AphiCY6PO… <https://secure-web.cisco.com/1ES7m6_j-xtuKVPJ2bSeckrMa9dywupWgezD1AphiCY6PO…>), and the Department of Computer Science at the ETH Zurich (https://secure-web.cisco.com/1lxmmD3IZNOWGQgMIQyHgzhT6k-IZxsdYUMVJGdRRZfNTk… <https://secure-web.cisco.com/1lxmmD3IZNOWGQgMIQyHgzhT6k-IZxsdYUMVJGdRRZfNTk…>). Workload %: 80 - 100% Qualifications: · MSc degree in a field related to cognitive neuroscience (e.g., cognitive neuroscience, (neuro-)psychology, computer science, biomedical or electrical engineering) · Deep knowledge in data science (time-series data processing, feature engineering and analysis) · Proficiency in programming (in Python, Matlab or R) is a must · Knowledge in mobile and wearable digital technologies is desirable · Experience with amyloid PET imaging and/or structural MRI analyses are a plus · Training in machine learning is a plus · Excellent verbal and written English skills Language requirements: English We offer: · To work in a team of highly motivated young researchers who are passionate about neuroscience, psychology and computer science · A very competitive salary (54’000 USD/year) and generous social benefits · Employment 3 years with the possibility of extension · Generous support for professional travel and research needs (~3’000 USD/year) · An inspiring work environment within the Department of Psychology and the University of Zurich and part of the Neuroscience Center Zurich (ZNZ) with many high-caliber collaborations (Department of Computer Science (ETH Zurich; Ce Zhang), Institute for Regenerative Medicine (UZH; Prof. Christoph Hock), Geographic Information Systems (UZH; Prof. Robert Weibel) · The opportunity to live in Zurich, one of the world’s most attractive cities Please visit https://secure-web.cisco.com/1Gd2AFC0ba61SE-PzvsUt26JL6je1tQ1bXlro3LofYXN_h… <https://secure-web.cisco.com/1Gd2AFC0ba61SE-PzvsUt26JL6je1tQ1bXlro3LofYXN_h…> for further information. This position opens on: 1.6.2022 (starting date) More information: Prof. Nicolas Langer, n.langer(a)psychologie.uzh.ch Application To be considered please stick to the following application format: · CV including publication list and contact details of two referees (max. 3 pages) · Statement describing motivations, personal qualifications and research interests (max. 2 pages) · Save application in one single pdf file with the file name “Methlab_[SURNAME]_[name].pdf” · Send application by email to: n.langer(a)psychologie.uzh.ch <file:///Users/nickilanger/Dropbox/AA_UZH_ADMIN/wichtige_dokumente%20&%20HR/Ausschreibung_PostDoc/n.langer@psychologie.uzh.ch> Applications will be considered until the position is filled (ideally submit your application before 31st of March 2022). Description of the Project: Real-life activity tracking as pre-screening tool for early stages of Alzheimer disease Alzheimer's disease (AD) accounts for the majority of all dementia cases and represents a major and rapidly growing burden to the healthcare and economical systems. The current state of research indicates that therapies need to be administered as early as possible. Therefore, there is an urgent need for accelerating biomarker discovery for early stages of AD. Importantly, evidences suggest that neurodegenerative changes precede clinical manifestations of AD by 20-30 years. However, prevailing potential biomarkers for early stages of AD diagnosis, including genetic testing, molecular examination of CSF, structural MRI and PET imaging, are highly limited as they can only be applied to relatively small sample sizes due to their excessive costs and invasive nature. This prevents their usage in large epidemiological studies; yet such study designs are imperative for identifying the intra-individual progression from healthy ageing to AD. Thus, novel non-invasive and inexpensive biomarkers are urgently required to be administered at large scale with the aim to identify individuals with indications for early stages of AD. These identified subjects could then be referred to undergo more cost-intensive examinations with the currently available biomarker techniques to achieve the desired diagnostic accuracy. Mobile and wearable digital technologies have an unprecedented potential and could close this current gap as they permit abundant, continuous longitudinal data acquisition at low costs to investigate intra-individual changes as early markers of AD. In this project, we will investigate whether activity measures, derived from GPS and accelerometer data, are sensitive to identify early stages of AD (i.e. mild neurocognitive disorder due to AD). Further, we aim to provide evidence that real-life activity measures are associated with current AD biomarkers (i.e. high Amyloid level and brain atrophy). Because our long-term vision is to develop a smartphone application that is able to identify intra-individual trajectories in healthy adults to establish the transition point to mild neurocognitive disorder due to AD as early as possible, we will examine the sensitivity of the real-life activity measures for intra-individual changes. Therefore, the present proposal serves as a proof-of-concept to address the prerequisites for real-life activity tracking as a pre-screening assessment tool to identify potential mild neurocognitive disorder patients. Nicolas Langer Professor of Methods of Plasticity Research University of Zurich Andreasstrasse 15 (Office AND.4.56) 8050, Zurich, Switzerland n.langer(a)psychologie.uzh.ch phone: (+41) 44 635 34 14 http://secure-web.cisco.com/1eprtfu6YVQ2Y3Wfp5VzOWnZz0Gm19H1RYpdVB_ZXOnH9Gb…

1 0

Tracula prepocessing error awk: fatal: cannot open file dmri/dwi_orig_las.1.bvals
by Vicente Ferrer 07 Feb '22

07 Feb '22

External Email - Use Caution Hi all, I was trying to run trac-all preprocessing and it seems there is a problem with eddy_openmp. The program is unable to find the dwi_orig_las.1.bvals file which makes that the index.txt is empty. see the terminal output: trac-all -prep -c tracula_config INFO: SUBJECTS_DIR is /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI INFO: Diffusion root is /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI Actual FREESURFER_HOME /share/opt/freesurfer-7.2.0 INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b trac-preproc -c /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/scripts/dmrirc.local -log /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/scripts/trac-all.log -cmd /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/scripts/trac-all.cmd #------------------------------------- /opt/freesurfer-7.2.0/bin/trac-preproc #------------------------------------- #@# Image corrections Mon Feb 7 15:56:50 CET 2022 rm -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvals /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvecs mri_convert --bvec-voxel /bcbl/home/public/PD_ANALYSIS/BIDS_DWI/sub-3102/ses-Session_baseline/dwi/sub-3102_ses-Session_baseline_run-_dwi.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz mri_convert --bvec-voxel /bcbl/home/public/PD_ANALYSIS/BIDS_DWI/sub-3102/ses-Session_baseline/dwi/sub-3102_ses-Session_baseline_run-_dwi.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz reading from /bcbl/home/public/PD_ANALYSIS/BIDS_DWI/sub-3102/ses-Session_baseline/dwi/sub-3102_ses-Session_baseline_run-_dwi.nii.gz... TR=900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1e-16, 0) j_ras = (1e-16, 0.92521, 0.379456) k_ras = (-3.79456e-17, -0.379456, 0.92521) writing to /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz... rm -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvals.tmp /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvecs.tmp mv -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvecs.tmp /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvecs mv -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvals.tmp /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvals orientLAS /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -7.86266 mri_convert -oni 116 -onj 116 -onk 72 -oid -1 1e-16 0 -ojd 1e-16 0.92521 0.379456 -okd -3.79456e-17 -0.379456 0.92521 -oc 2.02404 20.3466 -11.1417 -rt nearest /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.nii.gz mri_convert -oni 116 -onj 116 -onk 72 -oid -1 1e-16 0 -ojd 1e-16 0.92521 0.379456 -okd -3.79456e-17 -0.379456 0.92521 -oc 2.02404 20.3466 -11.1417 -rt nearest /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.nii.gz normalizing out_j_direction: (1e-16, 0.92521, 0.379456) -> (1e-16, 0.92521, 0.379456) normalizing out_k_direction: (-3.79456e-17, -0.379456, 0.92521) -> (-3.79456e-17, -0.379456, 0.92521) reading from /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz... TR=900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1e-16, 0) j_ras = (1e-16, 0.92521, 0.379456) k_ras = (-3.79456e-17, -0.379456, 0.92521) Reslicing using nearest writing to /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.nii.gz... INFO: found /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvals, copying INFO: found /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvecs, converting to LAS mv -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.nii.gz mv -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.bvecs /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.bvecs mv -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.bvals /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.bvals mri_convert --frame 0 /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/lowb_orig_las.nii.gz mri_convert --frame 0 /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/lowb_orig_las.nii.gz reading from /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.nii.gz... TR=900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1e-16, 0) j_ras = (1e-16, 0.92521, 0.379456) k_ras = (-3.79456e-17, -0.379456, 0.92521) keeping frame 0 writing to /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/lowb_orig_las.nii.gz... bet /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/lowb_orig_las.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/lowb_orig_las_brain.nii.gz -m -f 0.3 awk: fatal: cannot open file `/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.bvals' for reading (No such file or directory) eddy_openmp --imain=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.nii.gz --mask=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/lowb_orig_las_brain_mask.nii.gz --bvecs=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.bvecs --bvals=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.bvals --acqp=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/acqp.txt --index=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/index.txt --data_is_shelled --out=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi EddyInputError: Error when attempting to read --index file Terminating program Linux ipsnode-7-2.local 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Mon Feb 7 15:57:40 CET 2022 I checked the dmri directory and there is no dwi_orig_las.1.bvals. However there is a file named `dwi_orig_las.bvals`. Could the issue be that the file is not properly named? Thanks in advance Vicente Ferrer Predoctoral Researcher BCBL http://secure-web.cisco.com/1-Ku-hldgDaWjT-BvD-_pMWqml40Goi5g72COU-9PXhhnvl… Legal disclaimer/Aviso legal/Lege-oharra: http://secure-web.cisco.com/1nEcXGCtYms2UHA-p-uSmLLk_ufUH4B0eX4xXxtgSq9z_K3…

1 0

Re: [Freesurfer] virtual machine password
by fsbuild 07 Feb '22

07 Feb '22

External Email - Use Caution Sending to your email shortly. - R. On Feb 6, 2022, at 01:30, sina hospital <sina6312(a)gmail.com> wrote:        External Email - Use Caution        Greetings and RegardsPlease give me the ubuntu virtual machine passwordThanks_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

virtual machine password
by sina hospital 06 Feb '22

06 Feb '22

External Email - Use Caution Greetings and Regards Please give me the ubuntu virtual machine password Thanks

1 0

Re: [Freesurfer] Developer login
by fsbuild 05 Feb '22

05 Feb '22

External Email - Use Caution Sending the info to your email shortly. - R. On Feb 5, 2022, at 14:59, Guillaume Pech <mfb.pech(a)gmail.com> wrote:        External Email - Use Caution        Hello, I am installing Free-Surver via the VirtualBox and I need the password for the developer account please. Thanks _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Developer login
by Guillaume Pech 05 Feb '22

05 Feb '22

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer