Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

small numbers of extracted pial surface area‏
by Karl Liu 18 Mar '16

18 Mar '16

Dear Freesurfer experts, I am reposting my question from early this week since it is not answered. Any help much appreciated. My question is about the measure of pial surface area. Following a group comparison and correction in QDEC, I found a significant cluster (size: 760mm^2) when choosing area. pial as the measure. In order to plot group means in a bar graph, I extract numbers from the "cache.th20.neg.y.ocn.dat" file, but the average is less than 1. Why is the magnitude of supposed pial surface area so small? Is this actual or standardized measure ? Karl

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Reg: Correcting Defect error
by Jesu Kiran Jk 18 Mar '16

18 Mar '16

Dear Freesurfer experts, I have been running freesurfer for a patient data, and have to find this retesselalation of defect. I have successful with some data but for some others it looks frozen even after 7 days. Would it be possible to please have a look and help me out? Also, how could I pass on the data? Looking forward for your kind reply, Kind regards, Jesu

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Re: [Freesurfer] Extremely small numbers of extracted pial surface area
by Karl Liu 18 Mar '16

18 Mar '16

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GM mask to native T1
by Patrick Beukema 18 Mar '16

18 Mar '16

I am attempting to align the GM mask (lh.ribbon.mgz) to the T1 in native space. I see this thread that states this command is the correct way: mri_label2vol --seg lh.ribbon.mgz --temp rawavg.mgz --o ribbon-in-rawavg.mgz --regheader ribbon.mgz from: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33578.html However, when I do do, the alignment is off. All of my rawavg.mgz are rotated relative to the original T1 in native space, so the GM masks are also not properly aligned. Is there a transformation that I am missing somewhere between rawavg.mgz and native T1? Thank you, Patrick

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mri_glmfit
by John Anderson 18 Mar '16

18 Mar '16

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Per-vertex regression model
by Sophie Maingault 18 Mar '16

18 Mar '16

Hello FS experts, I would like to correlate for each vertex 2 anatomical variables (for example cortical thickness and surface area), i.e. doing a vertex-wise correlation between 2 maps for a cohort of subjects. Maybe it is possible with the command line mri-glmfit and with the argument "--pvr » for per-vertex regressors? Is that possible or not ? If yes could i have some extra information to use properly the command ? Thanks by advance, My best, Sophie Maingault - PhD Student IMN, Institut des Maladies Neurodégénératives, UMR 5293 Equipe 5 : GIN, Groupe d’Imagerie Neurofonctionnelle, CEA - CNRS - Université de Bordeaux Université de Bordeaux 146 rue Léo Saignat - CS 61292 - Case 28 33 076 Bordeaux cedex http://www.imn-bordeaux.org/ <http://www.imn-bordeaux.org/>

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Position Deep Learning of Neuroimaging in AD - Barcelona
by Juan Domingo Gispert López 18 Mar '16

18 Mar '16

The Barcelonaβeta Brain Research Centre (BBRC) welcomes applications for a full-time research position to develop deep learning methods to predict the onset of Alzheimer’s disease and its preclinical stage based on neuroimaging and other wet biomarkers, as part of its clinical research program. Qualifications: - PhD in Neuroscience, Medicine, Computer Science, Bioengineering or related disciplines (It is mandatory for the candidates to hold a PhD) - Proven experience in modelling and/or deep learning is required. - Strong understanding of the biological basis of AD and the course of AD biomarkers is needed. - Experience in neuroimaging and/or genetic data analysis would be positively considered. - Proven record of first authorship and co-authorship on scientific is required. Skills: - Experience working with large and multidisciplinary data sets is required. - Database manipulation skills, with strong attention to detail. - Proven ability to lead and orientate a team of computer scientists - Interest in joining a non-profit organization with a mission of high social impact. - Strong interpersonal skills (empathic and focused team-worker). - Ability to think independently and work collaboratively. Benefits: - Starting date: Second quarter 2016. - The research position is scheduled initially for two years (open to renewal). - Salary will depend on experience. In order to apply: To apply, please submit a single PDF file containing the following: 1) Cover letter describing research interests and relevant background; 2) CV with list of publications; 3) The names of three individuals who could provide reference letters. All files or inquiries should be submitted electronically to: cminguillon(a)fpmaragall.org Deadline for submitting applications: April 29th 2016. -- Aquest missatge i els seus annexos poden contenir informació confidencial i exclusiva per al destinatari. El seu contingut no constitueix un compromís per part de l'emissor. Si rep aquest missatge per error, si us plau elimini’l sense revisar-lo ni reenviar-lo i notifiqui-ho al remitent. Gràcies per la seva col·laboració. *This message and attachments may contain confidential and exclusive information intended only for the individual named. The content of this message does not imply any commitment by the sender. If you have received this e-mail by mistake, please delete it before reading or distributing and notify the sender. Thank you for your cooperation.*

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mri_robust_register question
by Ji Won Bang 17 Mar '16

17 Mar '16

Dear. All. Hi. How are you? It might be a very naive question, but your advice is greatly appreciated! I'm trying to register 2 T1s obtained from 1 subject on different days and then register the functional scans to their corresponding T1s (registering the functional scans to the same day's T1). By doing so, I expect to get everything into the same space. (Each subject was scanned twice on two different days etc., day1 and day2) After running mri_robust_register onto day2's T1 as targetting day1's T1, I get v2to1.mgz (original T1 is 046.mgz). Then I'd like to run preproc-sess(that does registration as well) onto day2's functional scans. Is there a way to make preproc-sess do register functional scans of day2 to v2to1.mgz(of day2 that's created by mri_robust_register), not the original 046.mgz? The commands that I run are: recon-all -s $SUBJECT -all mri_robust_register --mov /home/jbang/Projects/replay/mri/replay10/mri/orig/046.mgz --dst /home/jbang/Projects/replay/mri/replay06/mri/orig/036.mgz --lta /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.lta --mapmov /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.mgz --weights /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1-weights.mgz --iscale --satit preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_sponta -per-run -force -fwhm 0 Please feel free to give me any advice! Thank you very much. Best, Ji Won

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HIRING: Research Assistant
by Rockers, Elijah D. 17 Mar '16

17 Mar '16

Hello, The Houston Methodist Research Institute is hiring for a research assistant position. Please see the attached document for details. Please also note that candidates must be able to work in the city of Houston day-to-day. If you are interested in applying, please follow the instructions enclosed. Thank you, Elijah Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Post-doctoral position available – Human Neurocognitive Aging
by Arnold Bakker 17 Mar '16

17 Mar '16

Post-doctoral position – Human Neurocognitive Aging The Johns Hopkins University School of Medicine, Department of Psychiatry and Behavioral Sciences, Division of Psychiatric Neuroimaging (PI: Arnold Bakker, Ph.D.) has a vacancy for 1-2 postdoctoral scholars to perform federally-funded research in the areas of learning and memory, aging, dementia and depression using human functional neuroimaging methods. As part of the research team, the candidate will be responsible for the design and implementation of behavioral and imaging experiments aimed at assessing learning and memory performance, or the effects of depression on learning and memory and cognition, broadly in both young and older adults and in individuals with memory complaints or mild cognitive impairment. Our studies focus primarily on the role of the medial temporal lobe and particularly the hippocampus in memory function, age- and disease-related memory impairment and neuropsychiatric conditions. We are also interested in neural network approaches to learning and memory, cognitive aging and intervention using studies of resting state activity and functional connectivity. The Division of Psychiatric Neuroimaging is affiliated with the Johns Hopkins Alzheimer’s Disease Research Center (JHADRC), the Division of Geriatric Psychiatry and Neuropsychiatry, the Kirby Center for Brain Imaging, the Center for Imaging Science (CIS) and the HOPE4MCI study. These affiliations and the Johns Hopkins community in general provide a rich and unique environment for collaboration and education for candidates interested in learning and memory in aging and disease, and neuropsychiatry. The successful candidate will have a strong background in cognitive neuroscience and will have significant experience with functional MRI, as well as a background in learning and memory. A Ph.D. in Neuroscience, Cognitive Science or Psychology is required. The successful candidate should also have excellent writing and communication skills and be willing to learn new MRI analysis methods. Salary will be dependent on the experience of the individual candidate. To be considered, please send a letter of interest including a brief description of research interests, a curriculum vitae including a record of research accomplishments, and the names of three professional references to Dr. Arnold Bakker (abakker(a)jhu.edu<mailto:abakker@jhu.edu>). -- Arnold Bakker, Ph.D. Division of Psychiatric NeuroImaging Department of Psychiatry and Behavioral Sciences The Johns Hopkins University School of Medicine 600 N. Wolfe Street / Phipps 300 Baltimore, MD 21287 Phone: 410-502-6944 | Fax: 410-614-3676

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Freesurfer March 2016