Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Surfaces with different numbers of vertices.
by Nillo, Ryan Michael R 01 Jul '19

01 Jul '19

Hello Freesurfer users/developers, I have surface with ~73,400 vertices generated from the Freesurfer version 6 fsaverage brain, left hemisphere. I have a surface map that was created by mapping a volume to the fsaverage white surface. Is there a way to map the surface map to the new surface with less vertices? Is there a way to map values from the 73,000 vertices-map to the standard fsaverage pal surface? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging External Email - Use Caution

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Re: [Freesurfer] Question about OptSeq
by Greve, Douglas N.,Ph.D. 01 Jul '19

01 Jul '19

No, there is not. optseq assumes you will be doing an FIR analysis (=finite impulse response = not assuming a shape to the hemodynamic response). In this analysis, this must be the relationship. If you assume a shape, then this relationship is not necessary. In your case, you can set the dPSD=1. On 7/1/2019 7:19 AM, Davide Nardo wrote: External Email - Use Caution Dear Prof Greve, I hope you don’t mind if I ask you a question about OptSeq. It looks like a constraint in using OptSeq is that any event duration must be an integer multiple of the dPSD, which in turn needs to be an integer multiple of the TR, and seemingly there is no exception to this rule. I am in a situation in which my TR = 2 sec, and my event duration = 3 sec, therefore I get an error message when running OptSeq. However, I am puzzled by this, as in my experience with fMRI an event duration does not necessarily need to be a multiple of the TR… Is there any way I can circumvent this requirement in OptSeq? Best. Davide Nardo -- Davide Nardo, PhD MRC Cognition and Brain Sciences Unit University of Cambridge 15 Chaucer Road Cambridge, CB2 7EF Davide.Nardo(a)mrc-cbu.cam.ac.uk<mailto:Davide.Nardo@mrc-cbu.cam.ac.uk>

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[DEADLINE EXTENSION]: The 2nd International Workshop on Machine Learning in Clinical Neuroimaging (MLCN 2019): ENTERING THE ERA OF BIG DATA VIA TRANSFER LEARNING AND DATA HARMONIZATION
by MLCN Workshop 30 Jun '19

30 Jun '19

External Email - Use Caution Dear Colleagues,The submission deadline for MLCN 2019 workshop as a satellite event of the MICCAI 2019 conference has been extended to 14/07/2019. For more information, please visit https://mlcnws.com/call-for-papers/ . Call for Papers Recent advances in neuroimaging and machine learning provide an exceptional opportunity for investigators and physicians to discover complex relationships between brain, behaviors, and mental and neurological disorders. The MLCN 2019 workshop (https://mlcnws.com) as a satellite event of MICCAI 2019 (https://www.miccai2019.org) aims to bring together researchers in both theory and application from various fields in domains such as *e.g.* machine learning, neuroimaging, predictive clinical neuroscience, *etc.* Topics of interests include, but are not limited to: - Transfer learning in clinical neuroimaging - Model stability in transfer learning - Data prerequisites for successful transfer learning - Domain adaptation in neuroimaging - Data harmonization across sites - Data pooling – practical issues - Cross-domain learning in neuroimaging - Interpretability for transfer learning - Unsupervised methods for domain adaptation - Multi-site data analysis, from preprocessing to modeling - Big data in clinical neuroimaging - Scalable machine learning methods - Benefits, problems, and solutions of working with very large datasets SUBMISSION PROCESS: The workshop seeks high quality, original, and unpublished work on algorithms, theory, and applications of machine learning in clinical neuroimaging related to big data, transfer learning, and data harmonization. Papers should be submitted electronically in Springer Lecture Notes in Computer Science (LCNS) style ( https://www.springer.com/gp/computer-science/lncs/conference-proceedings-gu…) with up to 8-pages and using the CMT system at https://cmt3.research.microsoft.com/MLCN2019. The MLCN workshop uses a double-blind review process in the evaluation phase, thus authors must ensure anonymous submissions. Accepted papers will be published in a joint proceeding with the MICCAI 2019 conference. IMPORTANT DATES: - Paper submission deadline: July 14, 2019 (23:59 PST) - Notification of Acceptance: August 5, 2019 - Camera-ready Submission: August 12, 2019 - Workshop Date: October 13, 2019 Best regards, MLCN 2019 Organizing Committee <https://mlcnws.com/organization/>, Email: mlcnworkshop(a)gmail.com Website: https://mlcnws.com/ twitter: @MLCNworkshop <https://twitter.com/MLCNworkshop>

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Re: [Freesurfer] Longitudinal Masking and FDR
by Hua, Jessica 29 Jun '19

29 Jun '19

External Email - Use Caution Hi Kersten, I used this code to calculate the threshold: P = [ F_lhstats1.pval(lhcortex) F_rhstats1.pval(rhcortex) ]; G = [ F_lhstats1.sgn(lhcortex) F_rhstats1.sgn(rhcortex) ]; [detvtx,sided_pval,pth] = lme_mass_FDR2(P,G,[],0.05,0); pcor = -log10(pth) I substituted 0.1, 0.2, 0.5, 0.8, and 1 where the 0.05 is, and I kept getting the same pcor value of 4.8943. Jessica Hua

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mis-registartion question
by Nasiriavanaki, Zahra 28 Jun '19

28 Jun '19

Dear Freesurfers Hi I checked the functional to anatomical data registration using tkregister-sess -s $subj -fsd bold -per-run -bbr-sum. (The functional data is only collected from parietal and occipital lobes in 7T scanner). The values obtained from tkregister-sess are too high (0.95) for 7 out of 8 runs. When I looked at the snapshots obtained from QA_tools, they looked ok (top row images). But, when I looked at the volumes of the individual runs using tkregister2 command, the registration doesn't look good (bottom row images). tkregister2 --s $subj --mov /$subj/bold/011/template.nii.gz --surf --reg new.dat --regheader . I'm wondering if I need to do manual edits, and I appreciate any advice on that. Thanks Mona [cid:91ee52eb-c146-4bee-8cc8-19bf01ef7547][cid:487a26fa-1c27-4ed5-bd48-26a587d477d7] [cid:479ab0d3-00f7-406c-886c-4d83c945708e][cid:332d78df-9a82-4c35-a603-aa7a1734ba0f] Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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total cortical area
by Barletta, Valeria 28 Jun '19

28 Jun '19

Dear Freesurfers, Where in the /mri/stats folder can I find the total cortical surface in mm2? Is it in the ?h.aparc.stats or in the ?h.curv.stats? Thank you, Valeria

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How to account for gender in a contrast matrix
by Basavaraju, Rakshathi 28 Jun '19

28 Jun '19

External Email - Use Caution Dear all FS users, I wanted to know the way of accounting for gender in a simple regression analysis of cortical thickness against 2 continuous variables. Th example of contrast matrix given in the downloaded tutorial data for cortical thickness with age without accounting for gender is, 0 0 0.5 0.5 . However if we want to factor in gender how do we do it? Is it 0.5 0.5 0.5 0.5? or something else? Answers regarding same will be very much appreciated. Thanks, Dr. Rakshathi Basavaraju (MD Psychiatry) Postdoctoral Research Scientist Taub Institute Columbia University Irving Medical Centre 622 West, 168th Street, New York - 10032 E-Mail: rb3419(a)cumc.columbia.edu<mailto:rb3419@cumc.columbia.edu> http://www.wellcomedbt.org/fellowsprofile/dr-rakshathi-basavaraju-288

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Longitudinal Masking and FDR
by Hua, Jessica 28 Jun '19

28 Jun '19

External Email - Use Caution Hi FreeSurfer Experts, I had two questions regarding the longitudinal process. 1) I am using the linear mixed effects mass-univariate approach to analyze my longitudinal data. A priori I am interested in the orbitofrontal cortex and the parahippocampal gyrus. Is there a way in FreeSurfer to mask my longitudinal analyses to these regions specifically? 2) Also is there a way to modify the FDR2? My analyses do not meet the FDR2 (q < .05) p threshold of 4.29, and I wanted to see what threshold it is meeting. Specifically, I wanted to see if it was meeting q < .1. In the lme_mass_FDR2.m, I tried to change the rate to .1, but i kept getting the same result as when it was .05. Thank you in advance for your help! Best, Jessica Hua

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[Updated announcement] Postdoc position opening at Brown University in cognitive aging and Alzheimer’s disease
by Hwamee Oh 28 Jun '19

28 Jun '19

External Email - Use Caution We are seeking a highly motivated postdoctoral researcher to study behavioral and neuroimaging markers of preclinical Alzheimer’s disease in the Warren Alpert Medical School of Brown University. The primary performance site for this postdoctoral fellowship is in the Butler Hospital Memory and Aging Program (MAP). Brown University has a strong commitment to brain science and research in neurodegenerative disorders. This commitment is united under The Carney Institute for Brain Science and the new Center for Translational Neuroscience (CTN). The mission of the Carney Institute and CTN is to promote the discovery and innovation in brain science by supporting a diverse community of experimentalists, theorists, engineers, and clinicians. The MAP, one of the leading clinical trial centers for Alzheimer’s disease (AD) in the United States, is committed to accelerating drug and biomarker development for AD and to training young investigators for careers in AD research. The successful candidate will join a team of experts in Aging, Alzheimer’s disease, and related dementia research. This postdoctoral position is primarily focused on the area of the cognitive system in aging and preclinical Alzheimer’s disease and will work on developing early behavioral and neuroimaging markers of Alzheimer’s disease and integrating structural and functional MRI, PET, cognitive, genetic, and biofluid measures from ongoing or completed projects. Fellows will have ample opportunities to explore and gain experience with multidisciplinary and clinical research in aging and Alzheimer’s disease and to interact with core faculty members in the MAP and the Carney Institute of Brain Science at Brown University. Applicants with a Ph.D. degree in cognitive neuroscience, neuropsychology, biomedical engineering, electrical engineering, computer science, physics or a relevant field are encouraged to apply. Prior experience with human neuroimaging (e.g., task fMRI, rsfMRI, MRI, DTI, ERP, PET), a strong background in cognitive neuroscience and experimental design, and familiarity with programming in relevant languages (e.g., Python, MATLAB, C) are desirable. The successful candidate is expected to demonstrate communication skills, motivation and interest in the area of cognitive and brain aging, Alzheimer’s disease, and/or neuroimaging, and the ability to independently develop research questions and work in collaboration with other team members. The MAP is part of the Department of Psychiatry and Human Behavior at the Warren Alpert Medical School of Brown University, which is located in Providence, Rhode Island. Providence is within one hour from Boston and 3 hrs from New York City by train/subway and provides an intellectually and culturally rich environment with a reasonable living cost. Please note that this postdoctoral position is research-centered and prior clinical experience is not required. Pursuing licensure for a clinical neuropsychologist is optional. The postdoctoral position is supported by the fellowship program up to 2 years, with a possibility of support in year 3 depending on funding. *The expected start date is late Summer 2019; however, it is negotiable**.* Review of applications will begin immediately and continue until the position is filled. Interested persons can find more information on the position in the websites listed below. This postdoctoral fellowship is administered though the Research Fellowship Program within *The Alpert Medical School of Brown University, Clinical Psychology Training Programs at Brown: A Consortium of the Providence VA Medical Center, Lifespan, and Care New England. * The program’s website is located here: https://www.brown.edu/academics/medical/about/departments/psychiatry-and-hu… A full description of the fellowship position can be found in the link below: https://www.brown.edu/academics/medical/about/departments/psychiatry-and-hu… Details regarding application are located here under “Application Details”: https://www.brown.edu/academics/medical/about/departments/psychiatry-and-hu… NOTE: As explained on the application page of our website, applications are submitted through the APPA CAS portal. Instructions are located on the webpage. *****Prior to APPA CAS application submission, interested applicants are strongly encouraged to send a brief description of their research background and career goals, CV, and a list of three references to Dr. Hwamee Oh via email **at hwameeoh(a)gmail.com <hwameeoh(a)gmail.com>.* For any inquiries on the research and the position, please contact Dr. Hwamee Oh, the Director of Imaging Research in the MAP, at hwameeoh(a)gmail.com.

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Area information on certain views
by Kim, Jisoo,M.D. 28 Jun '19

28 Jun '19

Dear freesurfer team, I searched the archives, but couldn't find this kind of question. I've used the brainstem segmentation tool to get the volume of each brainstem structures, but now I am trying to get the area (mm^2) of midbrian and pons on mid-sagittal view. Do you know of an easy way to do this on FreeSurfer? Thank you. Best, Jisoo

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