Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30063 discussions

RFC: Changes to nibabel API for .mgh/.mgz files
by Christopher Markiewicz 31 Oct '17

31 Oct '17

Hi all, I'd like to solicit input for the Python interface to .mgh/.mgz files in nibabel[0]. I've recently had cause to dig into this interface (MGHImage[1]), and found that the naming of header fields[2] (analogous to variable names in C structs) is inconsistent with all of my experience with how FreeSurfer refers to these fields in the code (MRI_IMAGE[3]) as well as in the outputs of many programs, such as mri_info. (In fact, the current names seem to reflect the intermediate variables used in load/save_mgh.m and the description of the affine transforms in the FS Coordinates powerpoints[4].) I'm proposing (https://github.com/nipy/nibabel/pull/569) an API change in nibabel, with field names[5] that more closely reflect what I deem to be common FreeSurfer usage (although it does not adhere precisely to the C structure fields). Given that, it was felt that the FreeSurfer community more broadly should have some say in the final API. To put a few specific questions: Do you depend on the current MGHHeader field names? Would you be averse to updating the field names? If not, are there alternatives to my proposal you would find preferable? While I would be willing to discuss in more detail on this list, I don't want to needlessly pollute a support list with discussions of a third party API. If it's convenient, I would prefer responses on the pull request linked above. Thanks, Chris Markiewicz [0] http://nipy.org/nibabel/ [1] https://github.com/nipy/nibabel/blob/master/nibabel/freesurfer/mghformat.py [2] https://github.com/nipy/nibabel/blob/2139ce0d24e65a83295bb6b3eaaf005eaeaebb… [3] https://github.com/freesurfer/freesurfer/blob/master/include/mri.h#L157-L252 [4] https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems [5] https://github.com/effigies/nibabel/blob/55c9bf905ec8785617755f900635fc31ba…

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Re: [Freesurfer] Occiptial flattening
by Patricia Stefancin 31 Oct '17

31 Oct '17

Yes the lh.occip.patch.3d is in the surf folder for each subject.

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Occipital flattening
by Patricia Stefancin 31 Oct '17

31 Oct '17

In response to my previous question, the command line I was using was mris_flatten -1 -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat When I run this, the terminal output reads : lh.occip.patch.3d no such file or directory. I followed all the steps to create the patch, and saved the file with tksurfer. I don't know what could be going on.

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Using Freesurfer Recon1 with Brainvoyager QX
by Ashley A Presley 31 Oct '17

31 Oct '17

Hello, I am trying to use the skullstripping process of recon 1 to clean up the brains before importing into Brainvoyager QX. I convert the files to nifti in freesurfer then to VMR in Brainvoyager with the nifti gifti plugin. When I do this, however, the brain appears to be rotated and using Brainvoyager's manual spacial transformation makes the problem worse. I've attached a screenshot of the brainvoyager window after importing it through nifti gifti. Specs if needed: System: ubuntu 16.04 LTS Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c [cid:3FB7919ECFAE4272A3D7C63E5E71A258] NOTICE: This message, including all attachments transmitted with it, is intended solely for the use of the Addressee(s) and may contain information that is PRIVILEGED, CONFIDENTIAL, and/or EXEMPT FROM DISCLOSURE under applicable law. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or use of the information contained herein is STRICTLY PROHIBITED. If you received this communication in error, please destroy all copies of the message, whether in electronic or hard copy format, as well as attachments and immediately contact the sender by replying to this email or contact the sender at the telephone numbers listed above. Thank you!

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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

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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

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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.

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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/>*

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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

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