Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

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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Re: [Freesurfer] Total White matter and CSF value Calculation
by M Janani 09 Aug '17

09 Aug '17

Hi Douglas, Thanks for your support. From the below conclusion, can I say Total ventricular CSF = (lh + rh) Lateral-Ventricle + = (lh + rh)Inf-Lat-Vent + (lh + rh)choroid-plexus + 3rd-Ventricle + 4th-Ventricle + 5th Ventricle + CSF. Also Is it correct to compute Total CSF using the below mentioned formula Total CSF = Intracranial Volume - (Total white matter + Total Gray matter) Regards, Janani ---------------------------------------------------------------------------------------------------------------------------------------------------- Douglas Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Mon, 31 Jul 2017 07:48:02 -0700<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> On 7/31/17 3:12 AM, M Janani wrote: Hi Team, Could you please confirm whether the below mentioned formulas to compute Total WM and ventricular CSF are correct 1.Total White Matter = CerebralWhiteMatterVol + (lh+rh) Cerebellum White Matter looks right, though some times people will include brainstem as part of WM 2.Total ventricular CSF = (lh + rh) Lateral-Ventricle + = (lh + rh)Inf-Lat-Vent + (lh + rh)choroid-plexus + 3rd-Ventricle + 4th-Ventricle There is a 5th ventricle (which I think is basically the aqueduct). There is also a segment called "CSF" (24) but can't remember what gets labeled as "CSF" Thanks for your support. Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ---------------------------------------------------------------------------------------------------------------------------------------------------- _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer 6.0 and 5.3 differences in eTIV but not in supratentorial volume
by Lucette Cysique 09 Aug '17

09 Aug '17

Hello all FYI I have found non-negligeable differences in eTIV for 5.3 versus 6.0 in my healthy young sample It is probably due to the cerebellum computation changes (presented in released notes for 6.0) Unsurprisingly the supratentorial volumes 5.3 versus 6.0 are very similar (all was checked by simple correlations) Could people who have good knowledge of cerebellum studies comment on the reliability of freesurfer 5.3 in assessing size of the cerebellum versus manual tracing? This may need to be redone for version 6.0. Regards Lucette Lucette A. Cysique, Ph.D. NHMRC Clinical Career Development Fellow / UNSW Medicine 2013-2017 NeuroHIV and Quantitative Neuropsychology Group Leader @ NeuRA Senior Lecturer SoMs, UNSW Medicine Affiliated senior researcher at the St. Vincent's Hospital Sydney, Applied Medical Research Centre, Peter Duncan Neuroscience Unit Postal Address: Neuroscience Research Australia PO Box 1165 (Street Address: 139 Barker Street) Randwick NSW 2031 Australia Office Ph: +61 2 9399 1880 Mobile Ph: (+61) (0)431 576 710 (text preferred) Emails: lcysique(a)unsw.edu.au (primary) Lucette.Cysique(a)svha.org.au (St. Vincent's Hospital Sydney, related project) lcysique(a)ucsd.edu (HIV Neurobehavioral Research Center/UCSD related project) Twitter: @Lucette_C http://www.neura.edu.au/research/themes/cysique-group

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Urgent help with stats in FreeSurfer
by Martin Juneja 08 Aug '17

08 Aug '17

Hi, One of my papers is under review showing significant differences in cortical surface area between healthy controls and patients. In this paper, regarding statistical results, for multiple comparison correction, I ran Monte Carlo simulations using following command: mri_glmfit-sim \ --cache 4 neg \ --cwp 0.05\ --2spaces In the paper, I reported that multiple comparisons were corrected at p < 0.05 using Monte Carlo simulations. I also reported cluster sizes (number of voxels) of all clusters which survived multiple comparison correction. I checked literature and found that that's how people report cluster results after running analysis in FreeSurfer. One of the reviewers asked- Did you consider any constraints on findings (specifically cluster size) before considering the finding significant? Could you please help me in understanding this question and how can this be answered? In this paper: http://onlinelibrary.wiley.com/store/10.1002/pbc.25386/asset/pbc25386.pdf?v…, authors reported that - "The data were tested against an empirical null distribution of maximum cluster size across 10,000 iterations using Z Monte Carlo simulations as implemented in FreeSurfer [31,32] synthesized with a cluster-forming threshold of P < 0.05 (two-sided), yielding clusters fully corrected for multiple comparisons across the surfaces. Clusterwise corrected P < 0.05 (two-sided) was regarded significant." I assume that that's what reviewer is demanding me to report in my paper. I would really appreciate any help.

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Open position at Lausanne University Hospital: research and development engineer (fwd)
by Lilla Zollei 08 Aug '17

08 Aug '17

FYI ---------- Forwarded message ---------- Date: Mon, 7 Aug 2017 12:54:29 +0000 From: Meritxell Bach Cuadra <Meritxell.BachCuadra(a)unil.ch> To: Meritxell Bach Cuadra <Meritxell.BachCuadra(a)unil.ch> Subject: Open position at Lausanne University Hospital: research and development engineer Dear colleague, we are looking for a research and development engineer, for a one year position (extension of additional 6 months possible) at the Lausanne University Hospital, together with the Radiology and the Psychiatric Departments. The position is related to diffusion and functional MRI analysis and Connectome studies. Details and requirements are in the pdf attached. I would really appreciate if you could forward it to whom might be interested. Best regards, Meri Meritxell Bach Cuadra, PhD, M.E.R. Medical Image Analysis Laboratory (MIAL) - http://www.unil.ch/mial/ Department of Radiology, CIBM- Signal Processing Core - CHUV Unit University Hospital Center (CHUV) and University of Lausanne (UNIL) Rue du Bugnon 46, CH-1011 Lausanne, Switzerland Office BH 08-079, Phone: +41-21-314-67-75

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