Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30093 discussions

Cortical thickness from ROI in volume format
by Martin Juneja 01 Feb '17

01 Feb '17

Hi FreeSurfer experts, My goal is to extract cortical thickness of several ROIs, which are in volume space. I am following instructions from this page: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness My ROIs and T1 image are in the form of binary mask and are already in same standard space (MNIT1.nii). So following the instructions, I am able to perform until step 3 (I created registration file X.dat using fslregister command to register MNIT1.nii with fslaverage). After that I am using this command: tksurfer fsaverage lh inflated -overlay lh.fsaverage.ROI5.mgh -fthresh 0.5 to make sure that the ROI in surface format is at correct place. But after I run this command I do not see the region anywhere on surface. I tried to view it using FreeView also, its giving me attached image. From FreeView it looks like the ROI is now a brain mask and is all over the brain with a constant value everywhere. I am not sure why this is happening. Next, I have 26 ROIs, 12 on left hemisphere, 12 on right hemisphere and 2 in the midline. Somehow, 11/12 ROIs on left hemisphere and 2 ROIs in the midline are working fine when I view those in tksurfer or FreeView but rest all are showing me value of 1 all over the brain. For left hemisphere and midline ROIs, I am using exactly same steps as mentioned in the instructions but for right hemisphere, I just replaced 'lh' with 'rh' in step 3. Any help would be really appreciated.

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Announcing HCP Course 2017 at UBC in Vancouver June 19-23!
by Jennifer Elam 01 Feb '17

01 Feb '17

We are pleased to announce the *2017 HCP Course: "Exploring the Human Connectome"* <https://store.humanconnectome.org/courses/2017/exploring-the-human-connecto…>, to be held *June 19 – 23, 2017* at the University of British Columbia (UBC) <http://ubcconferences.com/>, in Vancouver, BC, Canada. This is the week before the Organization of Human Brain Mapping (OHBM) annual meeting <http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3734> to be held in downtown Vancouver (about 8 miles away from UBC) June 25-29. This 5-day intensive course will provide training in acquisition, processing, analysis and visualization of whole brain imaging and behavioral data using methods and informatics tools developed by the WU-Minn-Oxford Human Connectome Project (HCP) consortium. The course is designed for investigators who are interested in: - using data collected and distributed from the HCP young adult study - acquiring and analyzing HCP-style imaging and behavioral data at your own institution - processing your own non-HCP data using HCP pipelines and methods - using Connectome Workbench <https://www.humanconnectome.org/software/connectome-workbench.html> tools and sharing data using the BALSA <https://balsa.wustl.edu/> imaging database - learning HCP multimodal neuroimaging analysis methods, including those that combine MEG and MRI data - exploring the HCP MMP 1.0 <http://humanconnectome.org/about/pressroom/nature-article-cortical-brain-ma…> multimodal parcellation brain map and learning about how it can be used in your analyses - positioning yourself to capitalize on HCP-style data being distributed by the Connectome Coordinating Facility (CCF) from forthcoming large-scale projects (e.g., Lifespan HCP development and aging and Connectomes Related to Human Disease projects) Participants will learn how to acquire, analyze, visualize, and interpret data from four major MR modalities (structural MR, resting-state fMRI, diffusion imaging, task-evoked fMRI) plus magnetoencephalography (MEG) and extensive behavioral data. Lectures and labs will provide grounding in neurobiological as well as methodological issues involved in interpreting multimodal data, and will span the range from single-voxel/vertex to brain network analysis approaches. The course is open to students, postdocs, faculty, and industry participants. The course is aimed at both new and current users of HCP data, methods, and tools, and will cover both basic and advanced topics. Prior experience in human neuroimaging or in computational analysis of brain networks is desirable, preferably including some familiarity with FSL <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki> and Freesurfer <https://surfer.nmr.mgh.harvard.edu/> software. For more info and to register visit the HCP Course 2017 website <https://store.humanconnectome.org/courses/2017/exploring-the-human-connecto…>. If you have any questions, please contact us at: hcpcourse@humanconnectome. org We look forward to seeing you in Vancouver! Best, 2017 HCP Course Organizers

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Converstion of Wavefront .obj files into Nifti
by Dev vasu 01 Feb '17

01 Feb '17

Dear all, Could you please suggest me some method where i can possibly convert Wavefront .obj files into Nifti files, is such conversion technically relevant ?. Thanks Vasudev

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[FSFAST] Contrast percent map
by Seung-Goo KIM 01 Feb '17

01 Feb '17

Dear all, I wish to know how “cespct.nii.gz” is computed in selxavg3-sess. I thought it computes something like a relative change like: cespct = (contrast-baseline)/baseline*100, but I cannot figure out what was taken for the baseline. I thought it could be mean beta for constant terms (0-th polynomial) for each run, but my calculation was different from cespct. I would take average intensity for each voxel I would greatly appreciate a detailed explanation how the program computes it. Best regards, -- Seung-Goo KIM

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QDEC - Controlling for gender
by Jennifer Szeto 01 Feb '17

01 Feb '17

Hi Freesurfer experts, I am trying to compare cortical thickness between groups while controlling for age and gender using QDEC. However, gender is not showing up as a covariate variable or a nuisance factor (only showing up as a fixed factor), I am wondering how I could control for gender in this case? Thank you very much, Jen

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flip4fsl missing in stable6
by Fan, Qiuyun 31 Jan '17

31 Jan '17

Hi FreeSurfer experts, I figured 'flip4fsl' is missing from /usr/local/freesurfer/stable6/bin/. Can someone help to make a copy from /usr/local/freesurfer/stable5_3_0/bin/flip4fsl, if possible? Thanks a lot! Best, Qiuyun

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Neighborhood thickness in a 10mm radius
by Dorian P. 31 Jan '17

31 Jan '17

Hi Freesurfers, Thank you for the help you provide through this list. Is there a way to get, for each vertex, the identify (or thickness values) of the surrounding vertices in a 10mm radius? The command mris_convert has the '-v' option, but that produces only 5-6 vertices and there is no option to query a particular radius. I imagine this can be done manually outside Freesurfer by first identifying the neighbors for each vertex based on the coordinates, then getting the respective thickness value, but I wanted to check whether there is any easier way or any advice on how to proceed. Dorian

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Binary images multiplication
by Sahil Bajaj 31 Jan '17

31 Jan '17

Hi, I would like to multiply two binary images (standard brain image with an ROI) using fslmaths (or may be using some other way) command. Although both are in standard space but image dimensions are different. I was wondering if there is any way I can do that without any co-registration step. Thanks, Sahil -- -- ------------------------------------------------- Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. E-mail:sahil.brain@gmail.com <E-mail%3Asahil.phy(a)gmail.com>

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Postdoctoral Position in Division of Neurotherapeutics at MGH/HMS (Boston, MA)
by Afzal, Afsana 31 Jan '17

31 Jan '17

Hi everyone, The Division of Neurotherapeutics at Massachusetts General Hospital (Boston, MA) has an open postdoctoral position. The posting is below: NEUROIMAGING POSTDOCTORAL POSITION IN DIVISION OF NEUROTHERAPEUTICS AT HARVARD MEDICAL SCHOOL/ MASSACHUSETTS GENERAL HOSPITAL The Division of Neurotherapeutics at the Massachusetts General Hospital is looking for a neuroimaging postdoctoral fellow to join the research group of Drs. Darin Dougherty MD, Thilo Deckersbach PhD and Alik Widge MD PhD. Overview Research projects will focus on developing pipelines for multi-modal MRI analysis with the aim of investigating psychopathology along transdiagnstic domains under the TRANSFORM DBS project, using task-based and resting-state fMRI and structural MRI data. The post-doctoral fellow will have the opportunity to collaborate and work with an interdisciplinary team of clinicians, neuroscientists and engineers and have significant opportunities to advance their career. Your Profile We seek a postdoctoral candidate with a Ph.D. in psychology, neuroscience, or related discipline with an interest translational neuroscience with a strong background in Python, Matlab, or R. The ideal candidate would have extensive knowledge of computational neuroimaging. Expertise in cognitive modeling, graph theory, or machine learning is also highly desirable. Knowledge of common neuroimaging software, especially FreeSurfer and FSL, is also appreciated. Interest in understanding mechanisms underlying major psychiatric disorders and enthusiasm for working with psychiatric populations is necessary. Highly motivated individuals with a record of productive research are encouraged to apply. Benefits Benefits of this postdoctoral position include (1) access to numerous sets of high-quality, multi-modal MRI data; (2) opportunities to analyze and publish on these datasets; (3) mentoring for career development; and (4) access to imaging experts from around the world and to state-of-the-art tools for the development of neuroscientific and clinical research at the Martinos Center. Lab Description The Division of Neurotherapeutics at MGH is a multidisciplinary translational neuroscience group located at the Athinoula A. Martinos Center for Biomedical Imaging in Charlestown, MA. Our focus is on neurotherapeutic interventions for severe, treatment-resistant psychiatric illnesses, particularly for major depressive disorder, obsessive compulsive disorder, anxiety disorders, and eating disorders. Our research spans both mechanistic studies, clinical trials, and device-based interventions employing a variety of techniques, including neuroimaging and electrophysiology. We also provide clinical services and surgical treatments for psychiatric illness. Our work utilizes functional and structural magnetic resonance imaging (fMRI), positron emission tomography (PET), electroencephalography (EEG), magnetoencephalography (MEG) to further understanding of psychiatric illness and treatment. We use transcranial magnetic stimulation (TMS), vagus nerve stimulation (VNS) and deep brain stimulation (DBS) as tools to both treat disease and understand the neural correlates of mental illness. Lab Website: http://www.massgeneral.org/psychiatry/research/researchlab.aspx?id=1659 Contact: Afsana Afzal - aafzal(a)mgh.harvard.edu ______________________________ 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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Centre on label double click in freeview
by Chris Adamson 30 Jan '17

30 Jan '17

Thanks for putting in the "centre over label" feature in Freeview. Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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