Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Primary slice direction and image origin?
by falk.luesebrink＠med.ovgu.de 10 May '19

10 May '19

External Email - Use Caution Dear all, This is not directly related to FreeSurfer, however, can anyone tell me how the primary slice direction and image origin is determined from the DICOM header as displayed for example using mri_info? Best, Falk ............................................... [klinikum_logo_schmal_e-mail_blau] Universitätsklinik für Neurologie Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg Telefon: +49-391-6117-512 falk.luesebrink(a)med.ovgu.de<mailto:falk.luesebrink@med.ovgu.de> http://www.kneu.ovgu.de/kneu.html

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aparc.pial.stats
by Ting Li 09 May '19

09 May '19

External Email - Use Caution Dear Freesurfer Expert, Is there a way to get the aparc.pial.stats in one command like aparcstats2table? Thanks a lot! Best regards, Ting

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Fwd: Visualizing Volumetric Files on Surface
by Maedeh Khalilian 09 May '19

09 May '19

External Email - Use Caution > From: "Maedeh Khalilian" <M.Khalilian(a)sutech.ac.ir> > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Date: Thu, 09 May 2019 01:24:58 +0430 > Subject: Visualizing Volumetric Files on Surface > Dear FreeSurfer experts; > I have created some volumetric(.nii) files in FreeSurfer (the procedure > is > as following: lh/rh.aparc.annot> mri_divide_parcellation > > mri_aparc2aseg > > deleting subcortical and white matter regions in order to keep just > cortical > regions on GM). > > Now I wanna visualize my volumetric files on surface so that I myself > can > determine the color of each region. But I dunno how to do it exactly. > I would be grateful if u could help me with that. > Thanks in advance > Best regards > Maedeh, > >

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PostDoc position in Population Neuroimaging available, Connectivity Group, Research Centre Jülich (Germany)
by Svenja Caspers 09 May '19

09 May '19

External Email - Use Caution The Connectivity Group (lead: Prof. Dr. Svenja Caspers) of the Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich (Germany) is seeking applications for a *PostDoctoral Research Position in Population Neuroimaging* ** (E 13 TVöD; 39 hours/week) The Connectivity Group focuses on the investigation of brain variability throughout the life span in relation to environmental and genetic factors, with a particular focus on the aging brain and taking advantage of large population-based cohorts who underwent MR neuroimaging (e.g. UK Biobank, German National Cohort, Human Connectome Project, 1000BRAINS). Specific aspects include structural, resting-state functional connectivity as well as advanced diffusion imaging for structural connectivity analyses, including graph-theory analyses. Large cohorts of thousands of subjects are processed using adjusted pipelines and workflows for high-throughput imaging analytics based on common software packages (e.g. FreeSurfer, FSL, MRtrix) on available high-performance computing systems of the Research Centre Jülich. Current interests cover topics in advanced statistical analyses and data-driven methods using machine-learning and deep learning approaches. These efforts are part of current projects within the Human Brain Project (HBP). The successful candidate has a PhD in neuroscience, computer science, psychology, medicine or related fields and has experience with processing and analyses of MR neuroimaging data in larger cohorts. A strong interest and expertise in applying machine-learning to large neuroimaging datasets is highly desired to enable the candidate to conduct novel and innovative research projects to understand the normal variability of brain aging. Your profile: - deep knowledge of several software packages for processing of neuroimage data (e.g. FreeSurfer, FSL, MRtrix), also including respective python packages (e.g. NiPy, DiPy) and longitudinal pipelines - profound expertise in multivariate statistical analyses, including usage of software for large-scale statistical analyses (e.g. R) and modelling of non-linear and longitudinal effects - profound programming skills (e.g. Python) enabling high-throughput big data analyses - knowledge of and interest in machine-learning and deep-learning techniques to be applied to large neuroimage datasets of population-based cohorts - familiarity in working with large datasets - strong publication track record - ability to work independently - high proficiency in English The applicant will become part of an interdisciplinary team of PostDocs, PhD and MD students with various backgrounds. He / she will have ample possibilities to expand his / her own knowledge and expertise and interact and collaborate with colleagues from different fields, including big data analytics, genetics, epidemiology and microscopic analyses. With our group closely collaborating with the Jülich Supercomputing Center, the applicant will join current efforts in bringing population neuroimaging analytics to high-performance computing clusters for efficient and novel analyses approaches. The applicant will be involved in the supervision and mentoring of PhD, MD, master and bachelor students. Funding for the position is available for two years. Applications will continue to be received until the position is filled. Please send your comprehensive application, including CV, publication record, copies of relevant certificates and either reference letters or names of two potential references to Prof. Dr. Svenja Caspers (s.caspers(a)fz-juelich.de <mailto:s.caspers@fz-juelich.de>). -- ============================== *Univ.-Prof. Dr. med. Dr. rer. pol. Svenja Caspers * Direktorin Institut für Anatomie I Heinrich-Heine-Universität Düsseldorf 40221 Düsseldorf (Deutschland) Tel.: 0211-8112678 Email: svenja.caspers(a)hhu.de svenja.caspers(a)med.uni-duesseldorf.de /und / Arbeitsgruppe Konnektivität Institut für Neurowissenschaften und Medizin (INM-1) Forschungszentrum Jülich GmbH 52425 Jülich (Deutschland) Tel.: 02461-611742 Email: s.caspers(a)fz-juelich.de

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Questions about registration
by Yang, Weiqi 09 May '19

09 May '19

Hi, I am new to Free Surfer and am working on the resting state fMRI data analysis using FS-FAST. When I used the tkregister-sess command to see the registration quality (from structural image to fMRI image), I found that there is one registration not good (QA value = 0.9). So I did manual registration and save the reg. However, I don't know how to use my manual registration file as input for the bbregistration. My solution is that I overwrote the original registration file and ran the automatic registration again. Is there any neater way to do this? How to check the QA value for the updated registration? And I also found there are registration files in both fsd directory (ex. BOLD ) and the session directory (ex. 001). Are these registration files the same? Thank you in advance for your time. Best, Weiqi

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I: help segmentation
by Erika Portera 09 May '19

09 May '19

External Email - Use Caution ________________________________ Da: Erika Portera Inviato: giovedì 9 maggio 2019 09:08 A: freesurfer-request(a)nmr.mgh.harvard.edu Oggetto: help segmentation Good morning, I need your advice for a segmentation problem that I can't solve: I have noticed that FS does not recognize extracortical lesions (between gray and white) and tends to exclude them. I tried to include them with control points and adding voxel of white substance, following the tutorial, but the problem is not solved. Could you advise me? Thank you[cid:031365d1-0794-4660-a6d1-fdd3f6a9ad5f]

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Postdotoral call, human brain microstructure with MRI, Italy
by Jovicich, Jorge 09 May '19

09 May '19

External Email - Use Caution A 2-year postdoctoral call is available at the MRI Group of the Center for Mind/Brain Sciences (CIMeC) at the University of Trento, Italy. The focus of this position will involve the development, testing and validation of MRI techniques that allow quantification of function and tissue microstructure properties. The successful candidate will be part of an international multidisciplinary team developing and applying MRI techniques to study brain structure and function supporting normal higher cognitive function as well as the study of cognitive dysfunction in various neurological and neuropsychiatric conditions (including pre-surgical planning, plasticity in deaf and blind, novel markers sensitive to the progression of neurodegenerative diseases). Facilities: The CIMeC MRI neuroimaging lab uses a Siemens Prisma 3T scanner designed for research and clinical studies. The position will allow for training opportunities in pulse sequence development, brain anatomy, and translational clinical research. The fellow is expected to be able to work independently as well as part of a multidisciplinary team with supervisory responsibilities of graduate student research. The fellow will support research MRI users, will have opportunities to develop new ideas and advance their own research interests in an international academic environment. Beyond work, there are outstanding opportunities for enjoying outdoors activities. Requirements: Minimum qualifications are a doctoral degree in cognitive neurosciences, physics, engineering, computer sciences or related area, strong scientific publication record, and demonstrated expertise in MRI methods development and applications. The ideal candidates should be proficient in programming, such as C++, Matlab. Experience in pulse sequence design, particularly on Siemens platform, and/or image reconstruction will be a plus. Additional requirements include high self-motivation, ability of solving research problems independently, and excellent communication skills. Contact: Jorge Jovicich, Ph.D, MSc, Associate Professor (jorge.jovicich(a)unitn.it) Attending ISMRM, contact me for an informal meeting if interested Postdoc call: http://bit.ly/CIMEC-MRI-Postdoc-Call-2019 -- Jorge Jovicich, Ph.D. MR Lab Head Center for Mind/Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovicich(a)unitn.it MRI Methods Group: http://r.unitn.it/en/cimec/mri CIMEC: http://www.cimec.unitn.it/

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Job Opening: Research Associate Haskins Laboratories
by Meaghan Perdue 08 May '19

08 May '19

External Email - Use Caution Research Associate Job Announcement, May 2019: Research Associate Haskins Laboratories, 300 George Street, Suite 900, New Haven CT 06511 Project Director: Nicole Landi Qualified individuals are invited to apply for a full-time Research Associate position at Haskins Laboratories (https://haskinslabs.org) The successful candidate will join the labs of Professors Nicole Landi, Elena Grigorenko, and Kenneth Pugh which investigate the cognitive and neural bases of reading development and disability using behavioral and neuroimaging techniques (MRI, EEG and NIRS). This position will primarily involve analysis of MRI data; successful applicants will be involved in all aspects of the research process. Requirements include: - BA or BS in Psychology, Cognitive Science, Neuroscience or related field - Experience with structural or functional MRI data processing and relevant software (e.g., AFNI, SPM, FreeSurfer, FSL) Additional relevant skills include: - Programming experience (e.g., Python, Matlab) - Experience with statistical analysis (e.g., SPSS, R) - Experience with data management software (e.g., REDCap, Qualtrics) Interested applicants should contact Tammy Ursini, <ursini@haskins.yale.edu?subject=Lab%20Manager%3A%20Dr.%20Richard%20Aslin> Office Manager (ursini(a)haskins.yale.edu) with a cover letter, resume, copy of (unofficial) transcripts, and the names of three potential references. Please note “Landi Lab”, in the subject line of your email. The position will remain open until filled, with an anticipated start date of August 1, 2019 or sooner (a later start date is possible). Compensation is commensurate with skills and experience. Haskins Laboratories is a private, non-profit research institute with a primary focus on speech, language, reading, and their biological basis. Haskins has long-standing, formal affiliations with the University of Connecticut and Yale University. Haskins Laboratories is an Equal Opportunity Employer. -- Meaghan Perdue PhD Student Developmental Psychology Neurobiology of Language University of Connecticut Bousfield A302

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Visualizing Volumetric Files on Surface
by Maedeh Khalilian 08 May '19

08 May '19

External Email - Use Caution Dear FreeSurfer experts; I have created some volumetric(.nii) files in FreeSurfer (the procedure is as following: lh/rh.aparc.annot> mri_divide_parcellation > mri_aparc2aseg > deleting subcortical and white matter regions in order to keep just cortical regions on GM). Now I wanna visualize my volumetric files on surface so that I myself can determine the color of each region. But I dunno how to do it exactly. I would be grateful if u could help me with that. Thanks in advance Best regards Maedeh,

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Re: [Freesurfer] Cortex reconstruction using MRI with contrast
by Dengyu Wang 08 May '19

08 May '19

External Email - Use Caution Hi Bruce, My previous email with the wm.mgz and orig.nofix files was held by the system because of the big size. So in this email I attached some pictures about the wm and orig.nofix visualized in Freeview: Hope to get your opinion. Thank you! Best, Dengyu > On May 8, 2019, at 11:01 AM, Dengyu Wang <wangdy1995(a)gmail.com> wrote: > > Hi Bruce, > Thank you for your remind and I will keep in mind in the future. > > Here are the wm.mgz, lh.orig.nofix and rh.orig.nofix > > <wm.mgz> > <lh.orig.nofix> > <rh.orig.nofix> > > I tried to open in Freeview but Freeview always collapsed. > > Best, > Dengyu > >> On May 8, 2019, at 10:45 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >> >> Hi Dengyu >> >> I meant images of the brain. In general don't send us images of text - just send us the text so we can search and paste and such. In this case you have a huge defect that is probably caused by dura connecting to the wm. You need to look at the orig.nofix surfaces and the wm.mgz. You might need to make the skull stripping more aggressive and/or manually edit out some of the dura, but I can't tell without seeing the dataset. >> >> cheers >> Bruce >> On Wed, 8 May 2019, Dengyu Wang wrote: >> >>> External Email - Use Caution >>> Hi Bruce, >>> Thank you for your reply! And here is the detail: >>> >>> I use the command below to start the reconstruction: >>> >>> >>> >>> 366 defects are found in the process: >>> >>> >>> >>> And then says 281 defects to be corrected, and starts correcting the defect: >>> >>> >>> And then it gets stuck in correcting defect 46 and can’t move on: >>> >>> >>> We won’t have problem with t1 image without contrast, but in this special case we only have t1 with contrast. Do you have any ideas about this problem? Thank you! >>> >>> Best, >>> Dengyu >>> >>> >>> >>>> On May 7, 2019, at 4:37 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >>>> Hi Dengyu >>>> you need to tell us what went wrong. We have reconned lots of brains with contrast, although sometimes the skull stripping needs to be played with to get it to work >>>> cheers >>>> Bruce >>>> On Tue, 7 May 2019, Dengyu Wang wrote: >>>> >>>>> External Email - Use Caution >>>>> Hello FreeSurfer developers, >>>>> I am writing to ask about problem I met when reconstructing cortex from MRI with contrast? I had one subject that had only with contrast MRI images, and the recon-all can’t finish successfully. Is there any method or parameter setting that can solve the problem? Thank you! >>>>> Best, >>>>> Dengyu >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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