Freesurfer October 2017

freesurfer@nmr.mgh.harvard.edu

119 participants
179 discussions

Qdec and Brodmann regions
by Mohamed Ali Bahri 31 Oct '17

31 Oct '17

Dear Freesurfer experts, I would like to use "Qdec" tool to study the between groups changes of volume/cortical thickness of one region (Perirhinal) belonging to the Brodmann areas. As I understand Qdec load only the aparc and aseg stat lists. I am wondering if we could realty do that with "Qdec"? Any suggestion/advice will be very welcome. Many thanks in advance, Best regards, Mohamed -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Cyclotron Research Centre, University of Liège, Belgium m.bahri(a)uliege.be

1 1

Questions about BA template
by lanbo Wang 31 Oct '17

31 Oct '17

Dear experts, I have questions about BA template: 1. What's different between BA and BA.thresh? 2. I want to check the size of each structure of BA and BA.thresh template. How can I got it? Thank you in advance. All best, Lanbo Wang

2 1

Extracting labels using mri_watershed
by Fereshte 31 Oct '17

31 Oct '17

Dear Experts, How is it possible to extract labels like scalp and skull using -LABEL flag in mri_watershed ? Thanks for your attention.

2 5

postdoctoral fellowship in developmental cognitive neuroscience
by Anthony Dick 30 Oct '17

30 Oct '17

$50K plus benefits postdoc in Miami, FL, two years. Please take a look! http://myweb.fiu.edu/adick/post-doctoral-fellow-positions/ -- Anthony Steven Dick, Ph.D. Associate Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Florida International University MM Campus AHC4 454 Department of Psychology and Center for Children and Families<http://www.ccf.fiu.edu/>, an FIU Preeminent Program<https://beyondpossible.fiu.edu/preeminent-programs/> 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: adick(a)fiu.edu<mailto:adick@fiu.edu>; Webpage: http://dcn.fiu.edu<http://dcn.fiu.edu/>; Join the SSHD<http://www.sshdonline.org/> ##### Check out the new book<http://www.routledge.com/9781138960039>: Dick, A.S., & Müller, U. (2018). Advancing Developmental Science: Philosophy, Theory, and Method. Taylor & Francis.

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Postdoctoral Position: Developmental Neuroimaging
by emma jane 30 Oct '17

30 Oct '17

The Program for Translational Research on Adversity and Neurodevelopment (P-TRAN) at The Pennsylvania State University is seeking a qualified postdoctoral researcher with expertise in human brain imaging, specifically magnetic resonance imaging (MRI)) with children and adolescents. This position is supported by a recently awarded NICHD Center Grant (i.e., a CAPSTONE Center for Multidisciplinary Research in Child Abuse and Neglect; PI: Dr. Jennie Noll) and will be based in the Child Maltreatment Solutions Network (http://solutionsnetwork.psu.edu/) and the Prevention Research Center (www.prevention.psu.edu) both of which are located on the University Park campus in State College, PA. The primary responsibility of this position will be to provide neuroimaging research support (e.g., experimental design, implementation and data analysis) to a longitudinal project that will consider the biological embedding of child maltreatment in multiple biologic systems (e.g., neuroendocrine, autonomic, genetic, epigenetic, immunologic) and the impact of embedding on health outcomes, including neurodevelopmental trajectories. Candidates must have a PhD in psychology, neuroscience, or an allied field, or have completed all requirements for a PhD by the time of appointment. Applicants must have expertise in human subjects MRI, preferably with developmental cohorts. Preference will be given to those candidates with experience working with children who have experienced maltreatment or other high-risk groups. The successful candidate will be expected to contribute to experimental design and co-ordination of the neuroimaging aspects of the project and data analysis. Candidates must demonstrate expertise in functional and structural MRI analysis methods using standard processing packages (e.g., SPM, AFNI, FSL, Freesurfer etc.) and experience with longitudinal and complex datasets would be advantageous. The postdoctoral researcher will also be expected to contribute to manuscript preparation and presentation of study-related outcomes at key scientific meetings. Extensive mentorship will be provided to the successful candidate in order to facilitate transition to an independent research career. This position will provide an opportunity to interact with several vibrant research communities at Penn State, including the Social Sciences Research Institute (www.ssri.psu.edu) and the Social, Life and Engineering Science Imaging Center (www.imaging.psu.edu) among others. The initial appointment will be for one year, with the possibility of renewal in subsequent years. Salary and benefits are based on NIH guidelines, commensurate with experience and qualifications. Interested candidates should upload a CV, cover letter, statement of research interests, and 2-3 relevant publications. In addition, applicants should arrange for 3 professional references to be submitted separately to Dr. Emma Jane Rose (Associate Director for P-TRAN) at emmajanerose(a)psu.edu. Review of applications will begin immediately and will continue until the position is filled. For further information about this appointment, please contact Dr. Emma Jane Rose at emmajanerose(a)psu.edu or 814-865-0114 <(814)%20865-0114>. Apply online at https://psu.jobs/job/69051 CAMPUS SECURITY CRIME STATISTICS: For more about safety at Penn State, and to review the Annual Security Report which contains information about crime statistics and other safety and security matters, please go to http://www.police.psu.edu/clery/, which will also provide you with detail on how to request a hard copy of the Annual Security Report. Penn State is an equal opportunity, affirmative action employer, and is committed to providing employment opportunities to all qualified applicants without regard to race, color, religion, age, sex, sexual orientation, gender identity, national origin, disability or protected veteran status. -- *Emma Jane Rose PhD.* *Assistant Research Professor & * *Associate Director for the **Program for Translational Research on Adversity and Neurodevelopment (P-TRAN)* *Edna Bennett Pierce Prevention Research Center* *The Pennsylvania State University* *308 Biobehavioral Health Building* *University Park, PA 16802* *www.prevention.psu.edu <http://www.prevention.psu.edu/>* *www.npscoalition.org <http://www.npscoalition.org/>*

1 0

mris_decimate missing for Mac
by Paula Popa 30 Oct '17

30 Oct '17

Hello FreeSurfer Developers, I am using the development version of FreeSurfer, both for Mac and Linux. I have noticed that mris_decimate is not included in the package for Mac, but it does exist for Linux. I would like to know what will happen with it? Will it be included in the Mac package soon or at least in the next stable version? Or has the command been renamed/changed? Thank you very much, Paula

2 1

Qdec for Brodmann Areas
by Mohamed Ali Bahri 30 Oct '17

30 Oct '17

Dear Freesurfer experts, I would like to use "Qdec" tool to study the volume/cortical thickness of one region (Perirhinal) belonging to the Brodmann areas. As I understand Qdec load only the aparc and aseg stat lists. I am wondering if we could realty to do that with "Qdec"? Any suggestion/advice will be very welcome. Many thanks in advance, Best regards, Mohamed -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Cyclotron Research Centre, University of Liège, Belgium m.bahri(a)uliege.be

1 0

Recons for Allen Brain Institute T1 images with v5.3 online
by Melanie Ganz 30 Oct '17

30 Oct '17

Hi, So here’s the Wiki page for the human Allen brain data recons: https://surfer.nmr.mgh.harvard.edu/fswiki/AllenBrainAtlas Right now there’s only the v5.3 recons, but the v6 recons are coming asap. Cheers, Melanie

4 4

dmrirc_v1
by 郑凤莲 30 Oct '17

30 Oct '17

Hi Professor， Thank you for publishing Freesurfer software. Now I am studying DTI using Freesurfer. And I am interested in the technology of TRACULA. But when I run it, I encountered an error about valid frame numbers, as shown in the picture. And there is my dmrirc file. Do you know which part is wrong? Have you met this error? My DTI data has 63 directions. I don't know how to correct it. I really appreciate your help. I am looking forward your reply. Thank you very much.

2 1

cortical/subcortical volume based analysis
by miracle ozzoude 30 Oct '17

30 Oct '17

Hello FreeSurfer experts, I want to perform a whole brain volume based group analysis for cortical and subcortical regions. That's something very similar to surface based group analysis for cortical thickness however, for volume. Is there a tutorial on how to do it? if yes, please can i get the link. If not, please can someone direct me how to go about doing it? My goal is to perform a group comparison between control and PD patients based on volume. Thank you very much. Best, Paul

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Freesurfer October 2017