Freesurfer August 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
233 discussions

question about effects of changing server and freesurfer versions IF the entire study is consistent
by STACEY M SCHAEFER 09 Aug '17

09 Aug '17

Hello Freesurfer experts, We have processed, hand-edited, and QA'ed over 130 subjects' scans with version 5.3.0 on a linux sci6 box, and extracted the atlas-based ROI values for cortical thickness, volume, curvature, etc. The servers need upgrading but there are still whole brain analyses to run. Will there be any issues if we have processed all subjects identically, but then run analyses on the data with an upgraded linux and freesurfer's latest version? Thank you for your guidance! Stacey Stacey M. Schaefer, Ph.D. Center for Healthy Minds University of Wisconsin-Madison 625 W Washington Ave Madison WI 53703 608-263-9321

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Sphere above a certain vetex
by Redwan Maatoug 09 Aug '17

09 Aug '17

Hi everybody, I have a .annot file and I would like to display a sphere above one certain vertex. (I know the coordinates of the vertex) Someone knows a way to do that ? Thank you very much, Redwan

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Matrix ill-conditioned error for dods thickness mri_glmfit analysis
by Sullivan, Danielle Renee 09 Aug '17

09 Aug '17

Hi FreeSurfer Experts, I am trying to run a dods cortical thickness analysis examining the interaction of group on a continuous variable while controlling for other variables. Specifically, I have 6 classes (gender by three groups [zero, one, two]). I am interested in the group interaction with a continuous variable while controlling for gender (among 4 other continuous variables). I set up my fsgd file (see attached) and contrast file (36 dimensions- F test): 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 [1 -1 0 1 -1 0]/2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 [1 -0 -1 1 0 -1]/2 and ran this command: mri_glmfit --y lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.mgh --fsgd fsgd.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forFSGD.152.thickness.08082017.txt dods --C /GLM_CONTRAST.MAT/Contrast.Male.Female.Age.PC1.PC2.PC3.GGT.RORAbySex.mtx --surf fsaverage lh --cortex --glmdir lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.glmdir But keep getting this error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.mgh --fsgd fsgd.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forFSGD.152.thickness.08082017.txt dods --C /Volumes/VA_Imaging/Projects/salat/2389_TRT/dmiller/GGT_CRP/GLM_CONTRAST.MAT/Contrast.Male.Female.Age.PC1.PC2.PC3.GGT.RORAbySex.mtx --surf fsaverage lh --cortex --glmdir lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Any idea on what I am doing wrong? Danielle R. Miller, Ph.D. National Center for PTSD VA Boston Healthcare System Jamaica Plain Boston University School of Medicine OFFICE: (857) 364-4022

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Extracting pial surface from manually pareclated atlas
by Almarshad F. 09 Aug '17

09 Aug '17

Hi freesurfer team I'm just wondering if there is any way to extract left and right pial from manually parecllated file apar+aseg .mgh I need to view them with the new parecellation file Thanks in advance Fatima

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GLM error - cannot read fsgd file for reading
by Nick Corriveau-Lecavalier 09 Aug '17

09 Aug '17

Hi Freesurfer team, I'm trying to run a GLM analysis with three groups (Controls, MCI, AD) with 0 covariables at the moment, but I would like to add two eventually. I've been following the tutorial on this link: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V, and when I write the command it says ''cannot open g3v0.fsgd for reading''. In my /subjects/fsgd file, there is my fsgd file, and my contrast file. Am I missing an additionnal file or something? Is the format of my files correct? If it can help, here's what my fsgd file looks likes: GroupDescriptorFile 1 Title OSGM Class Control Class SCD Class MCI Variables Input 3431566 CTL Input 3514091 CTL Input 4051959 CTL Input 4344061 CTL Input 4557550 CTL Input 7060373 CTL Input 7274924 CTL Input 7308293 CTL Input 7424803 CTL Input 7459501 CTL Input 7543023 CTL Input 7661810 CTL Input 8069157 CTL Input 8330218 CTL Input 8656527 CTL Input 8875385 CTL Input 9296157 CTL Input 3025432 SCD Input 3494204 SCD Input 3702154 SCD Input 3708747 SCD Input 3865361 SCD Input 4316663 SCD Input 4509950 SCD Input 4548020 SCD Input 4893763 SCD Input 5381177 SCD Input 5477234 SCD Input 5522727 SCD Input 6121388 SCD Input 6168985 SCD Input 6258913 SCD Input 6274286 SCD Input 6334263 SCD Input 6417837 SCD Input 6427603 SCD Input 7435733 SCD Input 7485585 SCD Input 7712552 SCD Input 8827943 SCD Input 8980899 SCD Regards, Nick Corriveau-Lecavalier, B.Sc. (Hons) Candidat au Ph.D. recherche/intervention, option neuropsychologie clinique Coordonateur à la recherche, Association étudiante des cycles supérieurs en psychologie de l'Université de Montréal (AÉCSPUM) Université de Montréal Centre de recherche de l'Institut universitaire de gériatrie de Montréal, bureau M7819

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multi-frame input error with PAR/SEC origin file
by Yagmur Ozdemir 19 09 Aug '17

09 Aug '17

Hello FreeSurfer experts, I am trying to run recon-all on a nifti file converted from PAR/SEC using dcm2niix, and this error came up pretty soon after the script started to run; >> mri_convert.bin /home/lab/Desktop/freesurfer/subjects/sub-06_run-01_T1w.nii.gz /home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/lab/Desktop/freesurfer/subjects/sub-06_run-01_T1w.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (-0, 0.916013, -0.401149) k_ras = (0, 0.401149, 0.916013) writing to /home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Aug 8 17:42:13 EDT 2017 Found 1 runs /home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! I am pretty inexperienced with FreeSurfer, but does this error mean I need to slice my file? I would really appreciate if someone could give me some ideas for commands to use. Thank you all! Best, Idil

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Gcuts erasing voxels within the ventricles
by Elijah Mak 09 Aug '17

09 Aug '17

Hi Freesurfer Team, I am using gcut to improve the skull stripping on some subjects. I noticed that it is also removing some of the voxels in the ventricles of the brainmask.mgz (picture attached). Is this normal behaviour? Thanks for your time. Best Wishes, Elijah

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RA/programmer job posting - neuroinformatics, big data {Disarmed}
by Gregory Book 09 Aug '17

09 Aug '17

The Olin Neuropsychiatry Research Center (http://nrc-iol.org <https://mail.hhchealth.org/owa/redir.aspx?SURL=uSa2XNwnKV8-7Rv8FVsBtiT8E_fT…>) located in Hartford, CT USA is looking for a research assistant II/data manager (or post-doc, depending on candidate) to assist with data management, neuroinformatics development, and big-data analyses. The Olin Center is a 40 person department, opened in 2003 at the Institute of Living. We have a Siemens Skyra 3T whole-body MRI, EEG, and TMS suites. The Olin Center's database of 30,000 imaging sessions also provides an internally accessible source of data for the candidate's own analyses, and a 350 node compute cluster with 0.5PB storage is available to use. We are looking for an RA or post-doc to help develop the Neuroinformatics Database (http://github.com/gbook/nidb <https://mail.hhchealth.org/owa/redir.aspx?SURL=G0CGaDyjxYvRJuzV1x96G6zCQEAo…> ), manage neuroimaging data, and assist with the programming of automated neuroimaging processing systems. The primary focus and approximately half of the position will be developing and maintaining imaging and non-imaging databases, but duties will also include responding to support requests, training, documentation, and bug fixing. The other half of the position will be analyzing data and contributing to manuscripts. Candidate is expected to have a bachelor’s degree (PhD for post-doc) and experience with at least 1 programming language. Attention to detail and database experience are very desirable. Experience programming PHP, Perl, HTML, SQL, in a Linux environment is strongly preferred. Neuroimaging experience is also preferred, but not necessary. Contact Greg at gregory.book(a)hhchealth.org <https://mail.hhchealth.org/owa/redir.aspx?SURL=noR_r6vL6Ge-Kyrlsf3Bvyk4VMdN…>

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Research Assistant Position at The Ohio State University
by Herring, Elizabeth J. 09 Aug '17

09 Aug '17

Research Assistant Position Clinical Neuroscience Laboratory Department of Psychology Ohio State University Applications are being sought for a full-time research assistant position, starting autumn semester 2017 in the Clinical Neuroscience Laboratory<http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html> of Dr. Ruchika Prakash at the Ohio State University. The laboratory is currently conducting several randomized controlled trials designed to look at the effects of lifestyle interventions, such as mindfulness training and exercise interventions on improving cognitive and emotional control in older adults and in individuals with multiple sclerosis. This position is designed for individuals with existing research experience who are interested in gaining knowledge in the new field of health neuroscience. Experience with programming and neuroimaging data analysis with FSL, AFNI, or SPM is strongly preferred. Responsibilities will include active involvement in all aspects of research, facilitating recruitment efforts between the laboratory and community partners, and overseeing day-to-day operations of the laboratory. If you are interested in being considered for the position, please apply online at https://www.jobsatosu.com,under job listing #430999 and submit a current CV, a brief statement of interest, and names of three references., If you have questions about the position or the lab, please contact Dr. Ruchika Prakash at prakash.30(a)osu.edu Lab Website: http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html The Ohio State University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status.

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PhD Scholarship at Aston Brain Centre (UK)
by King, Daniel (Research Student) 09 Aug '17

09 Aug '17

Dear Mailing List, Feel free to distribute the advertisement below for a PhD scholarship on an exciting machine learning project as you see fit. Best wishes, Daniel King PhD Candidate in Neurosciences, School of Life and Health Sciences & Aston Brain Centre (SW505), Aston University, Aston Triangle, B4 7ET West Midlands, UK Email: kingdj(a)aston.ac.uk<mailto:kingdj@aston.ac.uk> Twitter: @danieljking8 PhD Studentship - Computational modelling of brain images with lesions and their application to machine learning approaches to predicting child outcomes Life and Health Sciences - Studentships Contract Type: Fixed Term (for 3 years) Basis: Full Time Closing Date: 23.59 hours BST on Thursday 24 August 2017 Reference: R170352 Supervisors: Professor Amanda Wood, Dr Jan Novak & Dr Elaine Foley Applications are invited from highly motivated candidates for a project that will use advanced magnetic resonance imaging (MRI) methods to investigate traumatic brain injury in children. This opportunity is open to UK and EU students who have at least an Upper Second Class Honours degree (2.1) or equivalent in Computational or Physical sciences. The study will involve assessment of more than 800 children recruited in Birmingham and the overall study will examine Neuroimaging and Neurobehavioural data in nearly 1000 children. Analysis of the multimodal dataset will allow the construction of a model which will predict patient outcome after a traumatic brain injury allowing stratification of treatment and mitigate deficit. The successful candidate will join a multidisciplinary team who combine neurocognitive assessment with advanced image acquisition and analysis. It is expected that the candidate will have experience in computer programming using languages such as Matlab and/or Python and have some experience of image analysis and matrix manipulation. Aston University was ranked 5th out of 94 UK Higher Education Institutions for research in Allied Health Professions (REF 2014) and was ranked 1st for research environment. Additional information about research in the School can be found at http://www.aston.ac.uk/lhs/research/. Informal enquiries can be made to Professor Amanda Wood (a.wood4(a)aston.ac.uk<mailto:a.wood4@aston.ac.uk>) or Dr Jan Novak (j.novak(a)aston.ac.uk<mailto:j.novak@aston.ac.uk>). Financial Support: The studentship is open to Home/EU students only and comprises of a tax-free stipend at the 2017/18 RCUK rate of £14,553 p.a. and payment of Home/EU tuition fees only. The studentship is available for three years, subject to satisfactory progress review at the end of the first year, with an anticipated registration date of 1st October 2017. Application Requirements: Eligible Applicants should hold at least a Bachelor (Hons.) Degree of either 1st Class/ 2.1 or MSc/MRes in Computer Science, Engineering, Mathematics, Statistics or Physics. EU Applicants will need to demonstrate adequate proficiency in English Language skills, with a minimum overall score of 93 (Internet Based) (with a minimum score in each section of: R: 18, W: 23, L: 19 and S: 19) in TOEFL or IELTS with minimum marks of 6.0 in each section and an overall band of 6.5. Informal enquiries should be addressed to Professor Amanda Wood (E-mail: a.wood4(a)aston.ac.uk<mailto:a.wood4@aston.ac.uk>; Telephone: +44 (0) 121 204 3593) or Dr Jan Novak (E-mail: j.novak(a)aston.ac.uk<mailto:j.novak@aston.ac.uk>; Telephone: +44 (0) 121 (0) 204 3079). To apply please complete the on-line application form at http://www1.aston.ac.uk/lhs/research/postgraduate-research/apply/, choosing 'Research Full-Time Health Sciences September 2017' quoting the Reference: 'PhD_Wood PROBIt-1' on all applications. The Closing Date for all Applications is: Thursday 24th August 2017.

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Freesurfer August 2017