Freesurfer September 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
200 discussions

Cortical thickness to volume
by neuroimage analyst 14 Sep '16

14 Sep '16

Hi, Freesurfer Users. I tried searching for this question on the mailing list but couldn't get an answer. Hence, I am posting this here again. I ran the freesurfer analysis and got cortical thickness map for my group. I want to build an adjacency matrix by finding the correlation between the cortical thickness of various ROIs on an atlas (Either the default freesurfer atlas or AAL atlas). 1) How can I map the cortical thickness map to freesurfer template volume so that I can average the cortical thickness in the ROI to build the connectivity matrix? 2) Instead of mapping to freesurfer template, if I have to use AAL atlas can I simply map the cortical thickness map to MNI template and use AAL atlas in MNI template to carry out step (1). If yes, how should I go about doing that? I would appreciate any response. Thanks Regards!

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QA tools
by John Anderson 14 Sep '16

14 Sep '16

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convert FSFAST files to gifti format
by Sabin Khadka 14 Sep '16

14 Sep '16

Hi all, Is there a way to convert FSFAST files (fmcpr.odd.sm5.fsaverage.?h.nii.gz) files to convert into gifti format? I've tried mris_convert but it does not work. Thanks for help. Cheers, Sabin Khadka

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two postdoctoral positions at Florida International University, Miami, open immediately
by Anthony Dick 14 Sep '16

14 Sep '16

Dear colleagues--Please share widely, we are looking to hire immediately. Thanks! The S.E.L.F Regulation Laboratory (http://self-regulationlab.fiu.edu/; PI Dr. Paulo Graziano, PhD) in collaboration with the Developmental Cognitive Neuroscience Laboratory (http://dcn.fiu.edu; PI Dr. Anthony Dick, PhD) at Florida International University (Miami, FL) is seeking two postdoctoral fellows to participate in an NIMH funded study to examine the neurobiology of attention deficit hyperactivity disorder in young children with a particular focus on their executive function and emotion regulation functioning. Candidates should have a PhD in psychology, developmental science, neuroscience, clinical science, or related discipline. The project will use neuropsychological tests, psychophysiology, diffusion-weighted imaging, and functional magnetic resonance imaging on children 5-7-years-old (with and without ADHD), and thus experience in neuroimaging data collection and analysis, and excellent computational and statistical know-how, is highly desired. Experience working with young children with developmental disabilities is a plus, as is a clinical science background. The positions are for one year with the possibility of renewal for multiple years. Salary is $50,000 plus benefits. The positions are open immediately and we hope to fill them by November 1, 2016. FIU is a multi-campus public research university located in Miami, a vibrant, international city. It has a recently established medical school that emphasizes medical research and community based medicine, and a new imaging facility with a 3 Tesla Siemens Prisma scanner. FIU offers more than 180 baccalaureate, masters, professional and doctoral degree programs to over 50,000 students. Interested candidates should send application materials (curriculum vitae, sample publications, three references, and a letter describing research interests) directly to Dr. Paulo Graziano (pgrazian(a)fiu.edu) or Dr. Anthony Dick (adick(a)fiu.edu) Reviews of applications will begin immediately. -- Anthony Steven Dick, Ph.D. Associate Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidique Campus AHC4 454 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 Webpage: http://myweb.fiu.edu/adick Join the Society for the Study of Human Development: http://www.sshdonline.org

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colour scale
by Trisanna Sprung-Much 13 Sep '16

13 Sep '16

Hi there is there a way to view a colour scale bar in Freeview rather than Tksurfer, for instance, for a probability map? I can alter the Min and Max by "Configure Overlay" but cannot seem to display the bar next to my surface. Many thanks Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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Pial surface vs. aparc+aseg
by Nosal, Eryka [PSY] 13 Sep '16

13 Sep '16

Hi, I'm very new to Freesurfer, and I am trying to get subject-specific masks from the output of recon all that I can use on my functional data. I was going to isolate regions from the aparc+aseg files to create the ROIs. In my visual checks, I noticed that the pial surface often leaves off parts of the amygdala and hippocampus even though they are contained within the correct label of the aparc+aseg image. For my purposes, should I be concerned that these regions are not contained within the surface? Sincerely, Eryka Nosal Research Tech The University of Chicago Department of Psychiatry & Behavioral Neuroscience Clinical Neuroscience & Psychopharmacology Research Unit (CNPRU) Phone: (773) 834-4113 Website: http://cnpru.bsd.uchicago.edu/research.html ******************************************************************************** This e-mail is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this e-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is prohibited. If you have received this e-mail in error, please notify the sender and destroy all copies of the transmittal. Thank you University of Chicago Medicine and Biological Sciences ********************************************************************************

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Some volumes not loading (corrupted?)
by Rachel Romeo 13 Sep '16

13 Sep '16

Hi all, After doing some manual edits to the wm and pial masks, I recently had a recon fail with the following error: mghRead(/subject_177/mri/brainmask.mgz, -1): read error Invalid argument mri_em_register: could not open mask volume brainmask.mgz. When trying to load either the brainmask.mgz or wm.mgz into freeview, these also fail, e.g.: mghRead(/subject_177/mri/brainmask.mgz, -1): read error MRIread failed: Unable to read from /subject_177/mri/brainmask.mgz All other volumes load fine. Can you think of what I might have done to corrupt these volumes? And is there a way to revert to the most recent version, so that I don't lose previous edits? Thanks so much, Rachel

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cannot read white surface
by Claudia Dacquino 13 Sep '16

13 Sep '16

Hi freesurfers, I'm trying to create an average subject for GLM analysis from my group, using make_average_subject --out newtemplate and I got this error: Reading surface /media/TREKSTOR/SUBJ/newtemplate/surf/lh.white No such file or directory ERROR: could not read /media/TREKSTOR/SUBJ/newtemplate/surf/lh.white ERROR: make_average_surface Any ideas on what the problem is? Why cannot find white surface? I'm using 5.1 version, but I got the same problem with version 5.3. Thanks to all. Claudia -- Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia Laboratorio di Neuropsichiatria Dipartimento di Neurologia Clinica e Comportamentale IRCCS Fondazione Santa Lucia via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 51501575 web: http://www.neuropsichiatrialab.com <http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli>

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cannot read white surface
by Claudia Dacquino 13 Sep '16

13 Sep '16

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Job posting
by Ansgar Furst 12 Sep '16

12 Sep '16

DEPARTMENT OF VETERANS AFFAIRS Palo Alto WRIISC Special Postdoctoral Fellowship Program in Advanced Neuroimaging The Office of Academic Affiliations, Department of Veterans Affairs (VA), is now accepting applications for a two-year Postdoctoral Fellowship Training Program in advanced neuroimaging with an emphasis on Traumatic Brain Injury (TBI), Posttraumatic stress disorder (PTSD), cognitive impairment and chronic pain. The Fellowship can begin between January 1st and August 31st, 2017. This is a joint fellowship between VA Palo Alto War Related Illness and Injury Study Center (WRIISC) and the Department of Psychiatry and Behavioral Sciences at Stanford University. The VAPA-WRIISC-SFP site is linked to the two other WRIISC fellowship sites (Washington, DC, East Orange, NJ) as well as the VA Mental Illness Research, Education, and Clinical Center (MIRECC) fellowship program (based at Palo Alto) for didactic, academic, and research efforts. The Palo Alto WRIISC specializes in integrating anatomical/functional Magnetic Resonance Imaging (MRI) and Positron Emission Tomography (PET) to improve the diagnostic/prognostic value of neuroimaging in the clinical setting. The fellowship provides a unique opportunity to (a) receive training in Diffusion Tensor Imaging (DTI), functional Magnetic Resonance Imaging (fMRI), Voxel-based morphometry (VBM) and amyloid imaging from a team of experienced neuroimagers and (b) relate neuroimaging findings to clinical cases in consensus conferences with our team of neurologists, nurse practitioners, psychiatrists & psychologists. We are interested in the relationship between TBI/PTSD and a potentially increased risk for Alzheimer’s disease and have recently received funding to explore this question using amyloid PET imaging. Our team of investigators is also part of the Alzheimer’s Disease Neuroimaging Initiative (ADNI). There are additional opportunities to explore projects in psychology and dementia with WRIISC, MIRECC, and Stanford faculty. In collaboration with their mentors, fellows will develop and conduct a research project, publish and present findings, participate in grant writing, and utilize the latest technologies for research (5 MRI scanners including a brand new PET-MR unit). Applicants must be US citizens. The ideal candidate will have a Ph.D. in cognitive neuroscience, computer science, psychology, or a related discipline. Prior experience in neuroimaging is essential. Experience with Linux, MATLAB, SPM8/12, FreeSurfer v5.3.0 & FSL v5.0 is highly desirable and programming skills would be a big plus. A. To be eligible to apply for the WRIISC Fellowship Program you must hold a PhD in one of the above described disciplines and be able to provide evidence of U.S. citizenship. B. Applications must be received by December 1st, 2016. Applicants must submit: a) a letter confirming they can fulfill the eligibility requirements; b) a personal statement describing their interest in the Fellowship; c) 3 letters of recommendation; and d) a current curriculum vitae. These materials can be submitted directly to the PhD Fellowship Program Director: Ansgar Furst, PhD at ansgar.furst(a)va.gov. C. If the applicant is identified as the candidate of choice for this site, they will be required to produce all documents listed in the above section A and the following additional documents: Transcripts from all educational institutions VA Form 10-2850d, “Application for Health Professions Trainees.” For more information, please contact Ansgar Furst, PhD at the WRIISC Palo Alto Fellowship site, (650) 493-5000, "1", "1" then x68652 or ansgar.furst(a)va.gov. See also: http://www.warrelatedillness.va.gov/

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Freesurfer September 2016