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Job ad: Small animal MRI faculty position at U. of Delaware
by Timothy Vickery 26 Aug '19

26 Aug '19

External Email - Use Caution Assistant/Associate Professor, Behavioral Neuroscience University of Delaware: College of Arts & Sciences: Psychological & Brain Sciences Location: Newark, DE The Department of Psychological and Brain Sciences ( https://www.psych.udel.edu) at the University of Delaware invites applications for an Assistant or Associate Professor in Behavioral Neuroscience to begin September 1, 2020. We seek to hire a research scholar with a neuroscience background in small animal brain magnet resonance (MR) imaging within any area of research. Scholarly excellence is preferred above all else. Ideal candidates will have extensive experience in neuroscience-oriented MR research and demonstrate innovative scholarship, with research that complements or adds to existing faculty expertise. This is an outstanding opportunity for a scholar to join and strengthen the growing Department of Psychological and Brain Sciences and its research and teaching missions. The Behavioral Neuroscience area has faculty focusing on spatial memory, fetal alcohol spectrum disorders, developmental psychobiology, social information processing, behavioral epigenetics, developmental neuroimmunology and endocrinology, neurobiology of emotional behavior, and stress-related hormonal and arousal systems in PTSD. Other faculty members in the Clinical, Cognitive, and Social Psychology areas in the Department have several active research programs utilizing our human MRI scanner. There are also many collaborative and synergistic possibilities with existing researchers throughout University of Delaware’s colleges. The candidate should enjoy interacting and collaborating with a diversity of researchers and students from various disciplines. An innovative leader in research and teaching, the University of Delaware combines a rich historic legacy with a commitment to education and the latest in advanced technology. With external funding exceeding $200 million per year, the University ranks among the top 100 universities in federal R&D support for science and engineering. Enhanced by state-of-the-art facilities, research is conducted across all seven colleges and numerous interdisciplinary institutes and centers. Relevant staffed facilities on campus include the new 11,600 square foot Center for Biomedical and Brain Imaging (http://cbbi.udel.edu) housing a new 9.4T/20cm Bruker MRI for small animals and a 3T Siemens Magnetom Prisma for humans; an animal housing and research facility attached to the CBBI; a 103,000 square foot Health Sciences Complex; a 194,000 square foot Interdisciplinary Science and Engineering Laboratory; and the Delaware Technology Park, where entrepreneurial and academic research labs are co-located. The NIH-supported Delaware Center for Neuroscience Research in collaboration with Delaware State University, and the Delaware Health Sciences Alliance (DHSA), a partnership among the University of Delaware, Christiana Care Health System, Nemours/Alfred I. du Pont Hospital for Children, and Thomas Jefferson University, provide infrastructure and opportunity for innovative basic, clinical and translational collaborations. The University of Delaware is located in Newark, Delaware, which is only a short drive or train commute from Philadelphia, PA. UD is also within driving distance of New York City, Baltimore, Washington DC, the Poconos and some of the finest beaches in the country, making it an ideal location for day or weekend trips. QUALIFICATIONS Applicants for this position must have earned a Ph.D., have a history of high-level publications in behavioral neuroscience or related fields, and conduct fundable research. APPLICATION INSTRUCTIONS To apply, please visit the submission website at https://careers.udel.edu/cw/en-us/listing/ and search for job # 494146 Applicants should submit a cover letter, a statement of research, a current curriculum vitae, three representative publications, and contact information for three confidential letters of reference. Inquiries, but not application materials, should be emailed to Jeffrey Rosen, Chair of the Behavioral Neuroscience Faculty Search committee, jrosen(a)udel.edu. Review of applications will begin on October 1, 2019 and will continue until the position is filled. The Department of Psychological and Brain Sciences holds diversity, equity, and inclusion as important values. We view diversity broadly, including but not limited to an individual's race, age, ethnicity, gender identity, sexual orientation, socioeconomic status, disability status, beliefs, and culture, as well as how those identities intersect. Supporting diversity in our faculty, student body, and staff, as well as valuing and respecting diversity in our teaching, research, service, and clinical work, represent important priorities that contribute to the strength of the department. We encourage the open exchange of ideas from a variety of viewpoints in an environment of respect, collaboration, and fairness. We promote the principles of equity and inclusion within our department and beyond through recruitment and retention, graduate training, clinical work, research, service and teaching, as well as through open and productive dialogue. More broadly, the University of Delaware is also committed to inclusive excellence. The University of Delaware is an Equal Opportunity Employer which encourages applications from minority group members and women. The University's Notice of Non-Discrimination can be found at http://www.udel.edu/aboutus/legalnotices.html. Applications close: Open until filled

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Invalid license key error for Freesurfer 5.1
by An Lijun 25 Aug '19

25 Aug '19

External Email - Use Caution Hello Freesurfer developers, Right now I am trying to use Freesurfer 5.1.0. But the software showed ERROR “Invalid FreeSurfer license key found in license file”. We tried to apply license online, however, the license provided online is now for 6.0.0 version and it seems not applicable for 5.1.0 since I still got the same error message as before. May I ask how to get the licnese of 5.1.0? Thanks for your help! ------------------------------------------------------------------------------------------------------------------------------------------ Best Regards, An Lijun

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mri_vol2vol
by Rihana Rayan 25 Aug '19

25 Aug '19

External Email - Use Caution Dear FS users, I have performed recon-all on structural data and created ROIs (using mri_binarize), I want to mask functional data (GLM beta) with ROIs. To match the file sizes, I resampled the ROI.nii by performing the command: mri_vol2vol --mov ROI.nii --targ beta_01.nii --regheader --o ROI_in_beta.nii Multiplying ROI_in_mask.nii by GLM beta, results in NaN over some voxels. Can anyone help me solve the problem? Best regards, Rihana

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what is the right manual correction when ?h.white extends into gray matter
by Caroline Chwiesko 23 Aug '19

23 Aug '19

External Email - Use Caution Hello Freesurfer experts, I wrote a previous email about my issue that in many of my subjects I have spots where the ? h.white is extending too much into the gray matter after running recon-all. As I understood from a conversation from somebody else, [[Freesurfer] WM surface including too much gray matter], you are currently looking into whether default parameter adjustments in recon-all can fix this problem. Until then, it was recommended to edit those errors manually. My question is what editing technique should I use if I want to manually edit thesis type of errors? Removing the voxels that I think are gray matter from the white matter file using recon edit? I am a little confused about this because I noticed that the ?h.white boundary does not necessarily follow the wm boundary (see attached image), so I am wondering, if changes to the wm will fix the problem that I have. Thank you very much in advance! Carolin [image: Screen Shot 2019-08-06 at 1.32.16 PM.png]

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extra cerebral CSF
by Jared Nielsen 23 Aug '19

23 Aug '19

External Email - Use Caution I've seen some previous posts about a measure of extra cerebral CSF coming in the future. Is the measure now available, or is it still in the works? If it's still in the works, can an ETA be provided? Thanks, Jared

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TRACULA - OrientLAS issue for a subject
by Daniel Callow 23 Aug '19

23 Aug '19

External Email - Use Caution For reference, I think the issue had to do with the orientation of these two subjects. I added tome code to use 3dwarp -deoblique to the dwi_orig.nii.gz and then ran orientLAS and it worked this time. The only thing I am unsure about is if this will nulify the bvals and bvecs I have and ruin later preprocessing steps? This is the only solution to the problem I have found thus far though. *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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recon_all hires
by Nasiriavanaki, Zahra 23 Aug '19

23 Aug '19

Dear Freesurfer experts I am doing recon-all on one of my subjects and it seems that it's stuck for days and not going through. I even re-run it and it's still stuck at the same spot as before. I attached the log file and here is my command: recon-all -all -s $subj -i /$subj/anat/$run/mT1v2.nii -expert expertopts/expert.opts -hires -mail zn025 -parallel I appreciate any help. Thanks Mona 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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Help with using family as random effect in sibling study
by Hopkinson, Casey E 23 Aug '19

23 Aug '19

Hello! I am trying to generate significance maps for a paired-difference analysis of cortical thickness using multiple pairs of siblings, and was wondering if there is a way to incorporate the family ID as a random effect/covariate in Freesurfer. Is it possible for the family ID for each sibling pair to be used as a categorical/discrete variable to then see the effect of family on cortical thickness in addition to the main effects we are looking at? Any guidance would be greatly appreciated! Best, Casey -- Casey Hopkinson Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 02129 (p) 617.643.3215

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Converting surface coordinates to MNI coordinates
by Avi Gharehgazlou 23 Aug '19

23 Aug '19

External Email - Use Caution Hi, I am conducting a meta-analysis on papers that have looked at local gyrification index (lGI) in Autism Spectrum Disorder (ASD) relative to typically developing (TD) peers. All lGI papers have used the FreeSurfer software and have reported x,y,z coordinates for their significant clusters (in which lGI in ASD is different from TD). Please help me with the below 2 questions: 1. My understanding is that these coordinates reported in lGI papers are "surface coordinates" (of fsaverage). Is this correct? 2. How can I convert these x,y,z surface coordinates to MNI space coordinates? I'd really appreciate your reply, Thanks so much, Avi

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Gender and age based reconstruction
by Carissa Liana Grijalva 23 Aug '19

23 Aug '19

External Email - Use Caution Hello FreeSurfer Support, I reached out the other day about if there was a way to specify the data is from a specific gender or age during the recon all code, such as a tag at the end. I was told that there is not way to tell recon-all about demographics/subject meta data, and not to worry about this during recon-all, but instead add age and gender as covariates in the model later. Does this mean FreeSurfer automatically finds the right regions regardless of age or gender? Does this work based on gray/white matter thresholds or something similar, so regardless of the demographics of the brain, it find the right regions? Thank you for your time. Best, Carissa Grijalva -- *Carissa Grijalva* *University of Arizona * *Biomedical Engineering PhD Program* *Undergraduate Research Opportunities Consortium Scholar* *NSF WAESO Research Fellow* *Society of Hispanic Professional Engineers*

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