Freesurfer August 2016

freesurfer@nmr.mgh.harvard.edu

127 participants
198 discussions

Error with long_mris_slopes: Surface files do not exist
by Corriveau-Lecavalier Nick 18 Aug '16

18 Aug '16

Hello FreeSurfer developers, I am trying to run the long_mris_slopes command for surfaces. It worked well the thickness, but when I run it for surfaces, my terminal tells me that the surface file (lh.surface or rh.surface) is missing. It appears that all my subjects are missing those files. I've search the list and no similar error seems to have been reported. This is the exact command I used: long_mris_slopes --qdec /Applications/freesurfer/subjects/longitudinal_training/long_training.dat --meas surface --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time weeks --qcache fsaverage --sd /Applications/freesurfer/subjects/ I am running a on a OS X El Captain software, and the FreeSurfer version I am using is the most recent one. I also joined the recon-all.long of one of my subject (of the base, since I'm running longitudinal data), in case it could help. Regards, Nick

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Recon-all Correcting Defect 0
by Heidi Foo 17 Aug '16

17 Aug '16

Dear FreeSurfer team, I am currently running recon-all for my subjects but for 2 of them, it stops at correcting defect. Do you have any ideas how I can deal with this problem? Thanks. Regards, Heidi Foo

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Bad Coregistration - Left-Right Reversed
by Afzal, Afsana 17 Aug '16

17 Aug '16

Hi, I'm having trouble co-registering a bunch of subjects whose T1 is left-right reversed. While the orientation of the structural file in the NIfTI header is LIA and the orientation of the functional volume is LAS, visual inspection shows that the structural is left-right reversed. I then followed the steps outlined in https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal to rerun the reconstruction and re-registered the subject but the registration mincost value is still hovering around 0.9 even with the left-right reversed structural. I've tried running registration with SPM and FSL; neither method is able to register these subjects properly. With --init-fsl I get the following: WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 and with --init-spm I get: WARNING: bad orientation matrix (determinant = 0) in nifti1 file ... ... continuing. At this point I'm out of ideas to try out. This issue is occurring for over 170 subjects (data collected outside Martinos using non-siemens scanners). Any help would be much appreciated! Thanks, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

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malloc_error_break/ can't allocate region
by miracle ozzoude 17 Aug '16

17 Aug '16

Hello FreeSurfer team, While running monte carlo correction with 10000 reps (mri_mcsim) for the whole hemisphere, I received this error at 975 reps for the left hemisphere " 975 3197.9 0 mri_mcsim(25495) malloc: ***mmap(size=16777216) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error" What does this mean and how can I resolve it? Below was my mri_mcsim command line " mri_mcsim --o wholebrainanalysis/average/mult-comp-cor/fsaverage/lh/cortex --base mc-z --surface fsaverage lh --nreps 10000" Thank you Paul

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Hiring: Cloud and HPC Engineer at NIMH in Bethesda, MD
by Thomas, Adam (NIH/NIMH) [E] 17 Aug '16

17 Aug '16

NIMH is hiring a Cloud and HPC Engineer. Please spread the word! https://github.com/nih-fmrif/hpc_job_ad HIRING: CLOUD AND HPC ENGINEER The National Institute of Mental Health (NIMH) is the lead federal agency for research on mental disorders. NIMH is one of the 27 Institutes and Centers that make up the National Institutes of Health (NIH), which is responsible for all federally funded biomedical research in US. NIH is part of the U.S. Department of Health and Human Services (HHS). The NIH is a highly rated employer at glassdoor.com with very competitive salary and benefits packages. The Data Science and Sharing Team (DSST) is a new group created to develop and support data sharing and other data-intensive scientific projects within the NIMH Intramural Research Program (IRP). Working closely with the Office of Data Science the goal of the DSST is to make the NIMH IRP a leader in the open science and data sharing practices mandated by the Open Data Policy released by the White House on 9 May, 2013. We are building a team to make that happen. What you’ll do… --------------- BUILD You will work with a team of researchers and developers to build and deploy neuroimaging data processing pipelines for investigators within the NIMH IRP. You will collaborate with and contribute to other projects throughout the world that are building standards and tools for open and reproducible neuroscience (e.g. NiPy, BIDS, Binder, Rstudio). You'll have the resources of the NIH HPC Cluster at your disposal as well as additional help from the AWS cloud. All tools and code will be open source and freely distributed. TEACH You will work to bolster data science skills within the NIMH IRP by teaching courses to scientists on best data practices (e.g., Software & Data Carpentry) as well as accessing and using specific neuroimaging repositories (e.g. The Human Connectome Project, OpenfMRI, UK Biobank). QUANTIFY There is no use building tools for open science if no one uses them. Part of the job of the DSST is to measure data sharing and open science practices within the NIMH IRP and progress toward their adoption. This will include bibliometrics for scientific publications from the NIMH IRP and other measures of data sharing and secondary data utilization. You will provide crucial systems level support to the team in gauging this progress. Who you are… ------------ EXPERIENCED You should be very comfortable on the command line and have a rock-solid handle on one or more Unix-based operating systems. You should have some experience with distributed, high-performance computing tools such as Spark, OpenStack, Docker/Singularity, and batch processing systems such as SLURM and SGE. You should also have experience coding in modern languages currently used in data-intensive, scientific computing such as Python, R, and Javascript, as well as interfacing with a variety of APIs. PROVEN Ideally we would like to see a recent degree (BS, MS, or PhD) in a STEM field, but if you can prove you have an equivalent amount of expertise with your publications, projects, or github/kaggle ranking, we’re all ears. We are also interviewing students and part-time staff if you’re still working on your degree. DRIVEN Data science is moving fast – we’re looking for someone who can move faster. You should be a self-learner and a self-starter. Provide some examples of things you have worked on independently. How to apply… ------------- Email your resume, a cover letter, and a code sample that demonstrates you are all three of the above to: DATASCI-JOBSEARCH(a)mail.nih.gov The National Institutes of Health is an equal opportunity employer.

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opening at the University of Sydney
by Anastasia Yendiki 17 Aug '16

17 Aug '16

---------- Forwarded message ---------- Date: Tue, 16 Aug 2016 22:55:47 +0000 From: Sasha Klistorner <sasha.klistorner(a)sydney.edu.au> Research Fellow - Neuroimaging Save Sight Institute and Brain and Mind Centre Sydney Medical School Reference no. 1332/0816 · Join a collaborative and supportive research team · Bring your expertise in neuroimaging to this important research in multiple sclerosis · Full-time fixed term for one year, remuneration package: base salary $99K-$117K p.a., leave loading and up to 17% superannuation The University of Sydney is Australia's first university and has an outstanding global reputation for academic and research excellence. It employs over 7600 permanent staff, supporting over 60,000 students. Save Sight Institute leads research into eye diseases and conditions, throughout Australia and internationally. Our renowned team of laboratory and clinical researchers are at the forefront of ophthalmic breakthroughs, and our findings have already saved the sight of many people living with eye disease since the institute was formed in 1985. The Brain and Mind Centre’s multidisciplinary research aims to set new standards in brain and mind sciences both in Australia and internationally, is dedicated to finding solutions that will lead to generational change. Our approach is based on the active collaboration of researchers from basic through to translational and clinical brain and mind sciences, students, patients and front-line carers. We are seeking to appoint a Research Fellow to work under the combined supervision of Associate Professor Alexander (Sasha) Klistorner at the Save Sight Institute and Associate Professor Michael Barnett at the Brain and Mind Centre. These world-class researchers are interested in the development of neuroimaging biomarkers of demyelination and axonal loss and the study of the mechanisms of axonal degeneration in multiple sclerosis using the visual system as a model. You will have the opportunity to actively participate in research in this area. In this role you will: * work closely with clinical, scientific, imaging and other relevant university staff at the Save Sight Institute and the Brain and Mind Centre, and the Sydney Neuroimaging Analysis Centre to develop and/or refine magnetic resonance imaging protocols and analysis pipelines relevant to the project * be required to develop and implement a tool for the longitudinal analysis of diffusion tensor imaging (DTI) alterations in multiple sclerosis patients * provide expertise across aspects of magnetic resonance imaging acquisition, protocol design and writing, analysis and interpretation of data relevant to the project; and contribute to writing peer-reviewed manuscripts * take responsibility for the supervision of research assistants / image analysts working on the project or related projects where relevant · undertake administration relating to your own university activities. You may also have the opportunity to work on other related team projects and to supervise postgraduate research students or projects and be involved in research training. To succeed in securing this role you will have: · a PhD in neuroimaging or a related discipline · knowledge of MRI analytics, physics, mathematical and computational modelling · strong experience in MRI image processing and analysis · solid experience in basic neuroimaging toolboxes such as FSL, FreeSurfer or similar analytical packages · experience in Diffusion MR data analysis · demonstrated experience writing complex analytical reports and papers · ability to work both independently and as part of a multidisciplinary team · programming skills in bash-scripting, Matlab and/or Python · sound organisational skills and ability to effectively manage competing priorities

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FA/MD.nii to fsaverage space
by Andrews, Derek 17 Aug '16

17 Aug '16

Dear Freesurfer developers, I would like to perform an analysis that requires me to have all of my subjects surface based and diffusion data in the same space. I have performed recon-all -qcache so that all my surface based measures are in fsaverage space. I now would like to register the FA.nii and MD.nii images to fsaverage space as well. Could you please provide me some command line examples to perform this? I am unsure if I should be using mri_vol2vol or mri_cvs_register. Thank you for your support. Best, Derek ________________________________ Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews(a)kcl.ac.uk

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Mixed anisotropic data
by Mahmoudi, Fariborz 17 Aug '16

17 Aug '16

Dear Friends, I have used a mixed set of images from 1.5T and 3.0T scanners with anisotropic voxel size in my study. I used Freesurfer tools for converting them to isotropic voxel size before segmentation and reconvert to initial state after segmentation. It is appreciated if someone let me know using such a mixed anisotropic data causes any side effect in the volume measurement or not. I will be also thankful if you could introduce a reference that discusses the effect. Best Regards, Fari ________________________________ CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies. Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy & Security page on www.henryford.com for more detailed information as well as information concerning MyChart, our new patient portal. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us.

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error in manual edit by freeview
by 陈聪 17 Aug '16

17 Aug '16

Hi dear all I am using freeview to edit segmentation, I found one slice in coronal view in brainmask.mgz mismatch with other slice, this slice obviously move down. WM and T1.mgz are normal, I don’t know how to move this wrong slice back. Any advice will be appreciated. thanks very much. CONG

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recon-all version update not showing in log file
by Donna Cosgrove 17 Aug '16

17 Aug '16

Hi, I am updating previously recon'd datasets done with FS versions 4.4 and 5.2 to v5.3. I'm running the recon-all command on the previously done subjects to retain any edits. However, when I had a look at the recon-all.log, it still has a date from the previous recon in 2013. The pctsurfcon.log contains this info (below) with an updated date, but nothing else seems to have updated... -------------- Logfile for pctsurfcon Sun Aug 14 06:12:59 IST 2016 setenv SUBJECTS_DIR /home/psych_lab/Desktop/freesurfer/FREESURFER_ DONE cd /home/psych_lab/Desktop/freesurfer/FREESURFER_D ONE /CON9231/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux nuig-79JP212-Ubuntu 3.13.0-43-generic #72-Ubuntu SMP Mon Dec 8 19:35:06 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer Cleaning up ------------- T he command I'm using recon-all -all -s SUBJ_ID seems to works fine, even identifying initially in the terminal that the build stamps do not match. It does also take much less time than a recon from scratch. Any thoughts would be appreciated. Thanks for your help! Donna

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Freesurfer August 2016