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30089 discussions

mri_surf2surf error
by mdkruepke＠uwalumni.com 01 Jun '12

01 Jun '12

To anyone who can help - I am trying to tun a GLM on a set of data and am currently receiving an error during the mri_surf2surf portion. When running this portion i receive an error ( could not scan # of lines from (path to rh.cortex.label)). This does not happen when running this portion for the lh, only the right. I am unable to find any information on this error on the mailing list so im hoping someone can help! Best- Michael Kruepke -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkruepke(a)gmail.com (262)-483-7449

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transfer annot files from template to each subject
by Leon 01 Jun '12

01 Jun '12

Hi, FreeSurfer expert I am having difficulty finding the functions that transfer an annotation file I generated on a template to each subject. This template has been registered with several subjects using a surface-based registration method. Now what I want is to (1) transfer this annotation file from the template to each subject, through surface-based registration. and then (2) transfer the annotation file in each subject's surface to their T1 volume space. Could someone show me which functions I need to use? Do I have to convert the annotation files first to label files to do that? Many thanks in advance Leon

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[Fwd: mri_glmfit error]
by YUMI MAEDA 01 Jun '12

01 Jun '12

HI, I figured out, one of the cope file had problem... YUMI HI, I am trying to see difference in groupmap between 2 time-point within 1 group with glmfit. I followed the instruction"PairedAnalysis". mris_preproc .... --paired-diff mri_glmfit --surf fsaverage "$hemi" --y "$hemi"_cope1_"$grp".sm"$fwhmsrc".mgh --yffxvar "$hemi"_varcope1_"$grp".sm"$fwhmsrc".mgh --glmdir $fsdir/group_surf//"$hemi"_cope"$num"_"$grp".sm"$fwhmsrc"_ffx --ffxdof 1872 --osgm When I checked the output of the mri_glmfit, the mask file does not cover the entire brain as the cope/varcope does. it is much smaller and missing parietal brain. the log file says "Reshaping mriglm->mask..." Is this the issue? YUMI _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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open Post-doc position
by Esther Walton 01 Jun '12

01 Jun '12

Post-doc position within the Collaborative Research Centre 940 "Volition and Cognitive Control: Mechanisms, Modulators, and Dysfunctions" at the Department of Child and Adolescent Psychiatry, University Hospital C. G. Carus, Dresden University of Technology, Germany PLEASE REPOST FOR INTERESTED PARTIES Job Description: The Department of Child and Adolescent Psychiatry, Dresden University of Technology, Germany invites applications for a postdoctoral research position in neuroimaging of eating disorders. The new project is part of the aforementioned Collaborative Research Centre (CRC, Steering Committee: Profs. T. Goschke, C. Kirschbaum, M. Smolka, A. Strobel, H.-U. Wittchen and will focus on cognitive control, reward system and the processing of emotions in patients with anorexia nervosa. This is a full time position within the Translational Developmental Neuroscience Group. Responsibilities will include the coordination of our ongoing clinical research study and the acquisition and analysis of a range of behavioral and magnetic resonance imaging (MRI) data. Together with a doctoral student new functional MRI paradigms need to be implemented. Imaging sessions will take place on the Neuroimaging Center's 3T Siemens TIM-Trio scanner and data collected includes high-quality structural, diffusion, and functional MRI data. A variety of additional information will also be collected, including neuropsychological and psychiatric scales, physiological and endocrinological markers. Summarizing results and writing research articles will be another central aspect of the work. The successful applicant will work in a team of young investigators and also be responsible to supervise doctoral students, interns and medical students working in the project. Thanks to the CRC the applicant will have ample opportunity to work with peers and senior scientists in similar project in the Medical School and the Psychology Department. Applicants for the position must hold (a) a PhD, MD or comparable degree in a relevant field (Psychology, Neurosciences or Medicine; if you have additional qualifications a degree in Biology, Biomedicine, Biophysics, Computer Science or Electrical Engineering may also be sufficient), (b) have had some exposure to cognitive and emotional neurosciences, (c) participated in research activities within the past years (d) published in peer-reviewed journals, e) possess strong organizational skills and (f) be able to communicate in German with non-scientific staff members. Some experience in computer programming (Linux/Unix shell scripting, Python and/or MATLAB), neuroimaging analysis methods (FSL, SPM, FreeSurfer or others), advanced statistical analyses and scientific publishing is necessary. The successful applicant will join a multidisciplinary team of researchers and clinicians, will receive further training and train doctoral students (informally). The position is available for a start date as soon as July 1st 2012 (to be confirmed). Review of applications will begin immediately and will continue until the position is filled. The position is guaranteed for one year with the possibility of renewal after positive evaluation. The CRC funding has been granted for 4 years. Salary will be consistent with levels in accordance with the German Research Foundation (100% TV-L: E 13). Compensation includes health insurance, and vacation time. To apply you can use our online portal (https://www.uniklinikum-dresden.de/Bewerbung/?id=81ed34303f2d9930fe6a6cb5d3… application should include a cover letter detailing professional objectives and interests, CV (with grades and language skills), and the names and email addresses of two references. The application can be written in German or English. Applications from many disciplines may be considered. The position is open to qualified international applicants but the knowledge of some German is necessary since the position includes the coordination of an ongoing clinical study. Applicants with a disability will be given preference in the selection process. Prof. Dr. med. Stefan Ehrlich Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie Universitätsklinikum Carl Gustav Carus Dresden an der TU Dresden E-Mail: KJPChefsekretariat(a)uniklinikum-dresden.de Please refer to our homepage: http://www.kjp-dresden.de/en/Eating-disorders, http://www.kjp-dresden.de/en/Schizophrenia and http://kjp-dresden.de/de/Publikationsliste-Prof-Dr-S-Ehrlich for more detailed information.

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open Research position (PhD)
by Esther Walton 01 Jun '12

01 Jun '12

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Re: [Freesurfer] long_qdec_table and LongQdecTable.py errors
by Martin Reuter 31 May '12

31 May '12

Great. Thanks for letting me know. I post this to the list, so that other know. Best Martin On May 31, 2012, at 21:11, Jiyagn <jiyang.jiang.email.lists(a)gmail.com> wrote: > Thanks for your reply Martin! > > I think I just found out where the problem was - a blank line at the end of the longitudinal table. The program works fine after deleting it. Probably the error is due to the different line break formats in Windows and Linux. > > Cheers, > Jiyang > > On 05/31/2012 10:39 PM, Martin Reuter wrote: >> Hi Jiyang, >> >> Must have missed Derin's mail. >> >> Can you send the table And command? >> I can then try to see if this bug is still in our dev version or if it got fixed in the meantime. >> >> Best Martin >> >> On May 30, 2012, at 22:06, Jiyang Jiang<jiyang.jiang.email.lists(a)gmail.com> wrote: >> >>> Hi Martin, >>> >>> I came across a problem when shrinking longitudinal qdec tables with 345 subject in two time points, into cross sectional form. The error states as follows: >>> >>> ------------------------------------------ >>> [jiyang@abc qdec]$ long_qdec_table --qdec ./long.qdec.table.dat --cross --out ./cross.qdec.table.test.dat >>> Parsing the qdec table: ./long.qdec.table.dat >>> Traceback (most recent call last): >>> File "/usr/local/software/freesurfer/freesurfer-5.1.0/bin/long_qdec_table", line 142, in<module> >>> longqdec = LongQdecTable(options.qdec) >>> File "/usr/local/software/freesurfer/freesurfer-5.1.0/bin/LongQdecTable.py", line 30, in __init__ >>> self.parse(stpmap) >>> File "/usr/local/software/freesurfer/freesurfer-5.1.0/bin/LongQdecTable.py", line 58, in parse >>> if strlst[0].upper() == 'SUBJECTS_DIR': >>> IndexError: list index out of range >>> ---------------------------------------------- >>> >>> I found Derin posted the same question on 20 Apr 2012, but it seems no following answers after. >>> >>> This error disappeared after deconstructing longitudinal qdec table. >>> >>> Any suggestion or clue will be appreciated. Thanks! >>> >>> Jiyang >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and properly >> dispose of the e-mail. >> > >

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pial mesh decimation...
by Gonzalo Rojas Costa 31 May '12

31 May '12

Hi: How can I do a decimation to 10000 polygons aprox to the pial surface ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Fwd: Harvard SEAS News: New master's degree in Computational Science and Engineering debuts (fwd)
by Bruce Fischl 31 May '12

31 May '12

FYI ---------- Forwarded message ---------- Date: Fri, 1 Jun 2012 00:27:36 +0000 From: Rosalind Reid <rreid(a)seas.harvard.edu> To: "aspuru(a)chemistry.harvard.edu" <aspuru(a)chemistry.harvard.edu>, "airoldi(a)fas.harvard.edu" <airoldi(a)fas.harvard.edu>, "David.Bear(a)gs.com" <David.Bear(a)gs.com>, "arb(a)lanl.gov" <arb(a)lanl.gov>, Michael P. Brenner <brenner(a)seas.harvard.edu>, David M. Brooks <dbrooks(a)seas.harvard.edu>, "dlb(a)lbl.gov" <dlb(a)lbl.gov>, "jchayes(a)microsoft.com" <jchayes(a)microsoft.com>, "davari(a)us.ibm.com" <davari(a)us.ibm.com>, "dietric(a)us.ibm.com" <dietric(a)us.ibm.com>, Ozlem Ergun <oergun(a)isye.gatech.edu>, "dfinkbeiner(a)cfa.harvard.edu" <dfinkbeiner(a)cfa.harvard.edu>, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>, "david(a)gilmour.net" <david(a)gilmour.net>, "jim.hurley(a)intel.com" <jim.hurley(a)intel.com>, "djj(a)io.harvard.edu" <djj(a)io.as.harvard.edu>, Gary King <king(a)harvard.edu>, "kou(a)stat.harvard.edu" <kou(a)stat.harvard.edu>, "dluebke(a)nvidia.com" <dluebke(a)nvidia.com>, L. Mahadevan <lm(a)seas.harvard.edu>, "joe(a)disneyresearch.com" <joe(a)disneyresearch.com>, "meade(a)fas.harvard.edu" <meade(a)fas.harvard.edu>, "chair(a)stat.harvard.edu" <chair(a)stat.harvard.edu>, John G. Morrisett <greg(a)seas.harvard.edu>, "papka(a)anl.gov" <papka(a)anl.gov>, Hanspeter Pfister <pfister(a)seas.harvard.edu>, "bruce(a)nmr.mgh.harvard.edu" <bruce(a)nmr.mgh.harvard.edu>, "Jeffrey.Saltzman(a)astrazeneca.com" <Jeffrey.Saltzman(a)astrazeneca.com>, Jeffrey Schnapp <jaytiesse(a)gmail.com>, Margo I. Seltzer <margo(a)seas.harvard.edu>, Sadasivan Shankar <Sadasivan.Shankar(a)intel.com>, "guy.steele(a)oracle.com" <guy.steele(a)oracle.com>, Christopher Stubbs <stubbs(a)physics.harvard.edu>, "streitz1(a)llnl.gov" <streitz1(a)llnl.gov>, Leslie G. Valiant <valiant(a)seas.harvard.edu>, "wakeley(a)fas.harvard.edu" <wakeley(a)fas.harvard.edu>, James H. Waldo <waldo(a)seas.harvard.edu>, Matt Welsh <mdw(a)mdw.la> Subject: Fwd: Harvard SEAS News: New master's degree in Computational Science and Engineering debuts Friends, I'm pleased to share the announcement issued by the School of Engineering and Applied Sciences today. Please feel free to share it with anyone! It will appear in the Harvard Gazette tomorrow. There is additional information for prospective students on the IACS website: http://iacs.seas.harvard.edu/master-of-science-in-cse. I'm happy to field inquiries from anyone interested in the program. Here's wishing everyone a wonderful summer. Ros ______________ Rosalind Reid Executive Director, Institute for Applied Computational Science Begin forwarded message: From: "Michael P. Rutter" <mrutter(a)seas.harvard.edu> Date: May 31, 2012 4:15:29 PM EDT Subject: Harvard SEAS News: New master's degree in Computational Science and Engineering debuts Contact: Michael Patrick Rutter, (617) 496-3815 Harvard to offer new master's degree in Computational Science and Engineering One-year master's, accepting applications this fall, ideal for students who wish to apply computation to academic and industry challenges Cambridge, Mass. ? May 31, 2012 ? A new master?s degree program in Computational Science and Engineering (CSE) will be launched at Harvard during the coming academic year, with the aim of training new leaders for a future where large-scale computation and advanced mathematical modeling will propel discovery and innovation in fields from psychology to photonics. The program, developed at the Harvard School of Engineering and Applied Sciences (SEAS), will begin accepting applications this fall, for enrollment in September 2013. Emphasizing the application of fundamental knowledge across the frontiers of natural and social sciences, humanities, and engineering, the one-year Master of Science (S.M.) program will provide rigorous training in the mathematical and computing foundations of CSE. Students will apply computation to chosen domains in independent research projects and elective courses. Beginning in 2014 SEAS will also offer a two-year Master of Engineering (M.E.) program, with a second year devoted mainly to research. ?Our aim is to create distinctive master?s programs that are both intellectually rich and scientifically vital,? said Cherry A. Murray, dean of the Harvard School of Engineering and Applied Sciences. ?It is essential that we provide the next generation of leaders with the heavy-duty computationalskills to analyze real, complex systems. We want to equip our students with the confidence to dive into fundamental problems like medicine, climate modeling, and operational logistics, and with the skills to reshape the world for thebetter.? The Harvard program will offer a curriculum broader than typical for master?s degrees in computational science, anchored by core courses in both computer science and applied mathematics and embracing a wide range of applications, including the social sciences in particular. New master?s students will engage with faculty from disciplines across Harvard?s departments in the arts and sciences so that all students are exposed to ideas and applications from many disciplines. The course of study, in fact, is intended to accomplish a set of eight learning outcomes developed with leaders in industry and the national labs, as well as faculty across Harvard. An advisory board, formed by SEAS dean Cherry A. Murray in 2010 to help design the program, agreed that graduates should be able to model complex systems, evaluate and implement efficient computational solutions, and collaborate to design robust software, and analyze massive data sets, among other objectives. Core courses focused on these outcomes are already being offered to Harvard students and proving popular. ?We at Microsoft Research New England very much look forward to deepening our collaboration and relationship with Harvard in this new endeavor,? said advisory board member Jennifer Chayes, Distinguished Scientist and Managing Director of Microsoft Research New England and Microsoft Research New York City. ?Many of the defining questions of this era in science and technology will be centered on ?big data? and machine learning. This master?s program will prepare students to answer those questions by integrating and applying computation and engineering with other disciplines, including both physical and social sciences.? Jointly managed by the Graduate School of Arts and Sciences (GSAS) and SEAS, the program has grown out of the recently created Institute for Applied Computational Science (IACS) in SEAS. IACS taps the diverse intellectual strengths of Harvard for insight into how torrents of data and new technologies are transforming scholarship and uses these insights in designing courses and student activities that achieve the program outcomes. The institute?s first milestone was the launch in 2011 of a Secondary Field, or graduate minor program, in Computational Science and Engineering,available to students currently enrolled in a Ph.D. program in GSAS. ?In keeping with Harvard?s emphasis on foundational knowledge, the master?s program will focus on crosscutting mathematical and computational principles. It will emphasize active learning, allowing students to implement and test these techniques in individual and collaborative projects in economics, physics, biology, and a range of other fields. This will prepare them to integrate critical knowledge in both industry and academic settings,? said Efthimios Kaxiras, the director of IACS and the John Hasbrouck Van Vleck Professor of Pure and Applied Physics in the Department of Physics and SEAS. Through their courses and projects, students who complete the program will acquire mastery of approaches including mathematical techniques for modeling and simulation ofcomplex systems; parallel programming and collaborative software development; and efficient methods for organizing, exploring, visualizing, processing, and analyzing very large data sets. ?Computer-aided in silico discovery and rapid prototyping will affect all areas of modern life by enabling modeling of complex systems: biotechnology for health; chemistry and materials discovery for aerospace, auto industry, clean energy, and information technology; behavioral economics for social sciences; and more,? said Sadasivan Shankar, Senior Principal Engineer and Program Leader for Materials Design at Intel. ?Harvard has again taken a leadership role in this shift by the inception of a multi-disciplined graduate program on application of computational sciences to areas of relevance to human advancement in the 21st century. We are very excited at this and hope to work with Harvard in promoting this journey.? Related activities organized by IACS will complement the coursework. The institute sponsors an ongoing lecture series and a High-Performance Computing Journal Club; it also hosts ComputeFest, a week of dynamic skill- and knowledge-building activities for the Harvard community each January. ?Los Alamos National Laboratory is delighted with Harvard's new master's degree program in CSE, and looks forward to a close relationship with the program through internships and reciprocal visits,? said advisory board member Alan Bishop, Principal Associate Director for Science, Technology, and Engineering at Los Alamos National Laboratory. ?There has been remarkable growth in advanced computing capability and impact in the U.S. over the last decade. The need to fully integrate this asset into the scientific method to enhance discovery, prediction, and design is evident in all disciplines as well as in the great complex systems challenges facing society, such as health, security, the energy-climate infrastructurenexus, and advanced manufacturing. Training the next generation of science,technology, and engineering leaders with the skills to formulate algorithmssuited for emerging computing architectures to accelerate progress is critical. Harvard is leading the way.? ## Students who apply for the CSE master?s program will be admitted through the Graduate School of Arts and Sciences (GSAS). For more information, visit the IACS website. About the Institute for Applied Computational Science The Institute for Applied Computational Science was established in September 2010 by the Harvard School of Engineering and Applied Sciences (SEAS). It is charged with launching a unique interdisciplinary education and research program in computational science and engineering (CSE). The new Institute will: * create an intellectual home for faculty and students applying computational methods to major challenges in science * enhance existing courses in applied mathematics and computation and develop new computational science courses, activities, and research opportunities for Harvard students from across the sciences. By establishing the Institute, SEAS has committed to fostering graduate training and research in applied computational science, infusing the curriculum with new courses and student research opportunities that will focus on the use of computation to power discovery and innovation. Frequently Asked Questions How do I apply to the program? Students will be admitted to the new program through the Graduate School of Arts and Sciences, which requires online submission of applications for graduate study. In general, applicants must hold the BA or equivalent degree. GSAS considers students for admission to the fall term only. Additional rules and requirements, including SEAS program requirements and the application deadline (generally December 15 each year), are outlined at the GSAS website. During 2012, applications will be accepted for the one-year S.M. program. The first applications for the M.E. program will be accepted in 2013 for enrollment in the fall of 2014. Students enrolled in the S.M. program will have the opportunity to apply at that time for thetwo-year program. IACS welcomes inquiries from all qualified prospective students interested in exploring the emerging field of computational science. For detailed information about studying CSE at Harvard, please contact IACS Executive Director Rosalind Reid. What is the difference between the secondary field and the master?s program in CSE? The secondary field is a four-course program available to Ph.D. students in GSAS. The S.M. degree requires eight courses and an oral examination. Students can either apply directly to the master?s degree program or take the master?s en route to a Ph.D. in another field. The M.E. will require a thesis and a total of 16 courses, at least six of which will be research courses. The M.E. is a terminal degree, meaning that students pursuing the M.E. cannot seek a higher Harvard degree. Can undergraduates with advance standing at Harvard apply to the program? Yes. Harvard College students admitted to advanced standing can apply to complete the S.M. in CSE during their senior year. What are the intended learning outcomes? The design of the program is based on eight learning outcomes, developed through discussions with the IACS Advisory Board. Each student's plan of study should address these outcomes. The outcomes answer the question: "What should a graduate of our CSE program be able to do?" 1. Produce a computational solution to a problem that is reproducible and can be comprehended by others in the same field. 2. Communicate across disciplines and collaborate in a team. 3. Model complex systems appropriately with consideration of efficiency, cost, and data availability. 4. Use computation for advanced data analysis. 5. Create or enable a breakthrough in a domain in science. 6. Take advantage of parallel and distributed computing and other emerging modes of computation, both in algorithms and in code implementation. 7. Evaluate and compare multiple computational approaches to a scientific challenge and choose the most appropriate and efficient one. 8. Apply techniques and tools from software engineering to build robust, reliable, and maintainable software. What are the degree requirements? Requirements for the S.M. degree address these learning outcomes. They build on the requirements already established for the Graduate Secondary Field in CSE. A total of eight courses are required. Each student's plan of study for the S.M. degree will include: * at least three of the four core courses, including 1?2 from the Applied Mathematics (AM) core and 1?2 from the Computer Science (CS) core * between two and six CSE electives chosen from the suggested electives list, including at least one from the AM list and one in CS * up to two ?domain electives??approved computation-intensive courses within a domain * up to two semester-length independent research projects * as a final requirement, an oral examination by a faculty committee S.M. course requirements (8 total) at a glance: S.M. requirements min max Core 3 4 Applied Math electives 1 3 Computer Science electives 1 3 Domain electives 0 2 299R research course 0 2 M.E. students will be expected to complete the full core along with additional domain electives and research courses. They will earn four course credits for thesis research. What sets the field of Computational Science and Engineering apart? Computational Science and Engineering (CSE), a rapidly emerging interdisciplinary field of inquiry, is an applied science, a mix of mathematics and computer science directed at Grand Challenge problems, from making solar energy affordable to providing access to clean water to improving urban infrastructures to securing cyberspace. At the same time, CSE has the potential to transform many fields, enabling new kinds of inquiry in protein folding, creating new materials, merging imaging and genomic data for medical applications, and simulating physical systems under extreme conditions that are otherwiseimpossible to study. Broadly, many fields in the natural and social sciences and critical areas in industry need experts in CSE who can create new ways of understanding, predicting, and solving problems. -- Michael Patrick Rutter Communications Director Harvard School of Engineering and Applied Sciences Pierce Hall 289, 29 Oxford Street, Cambridge, MA 02138 Work: 617-496-3815 | Cell: 617-216-1175 http://www.seas.harvard.edu Become a fan of SEAS http://www.facebook.com/hseas http://twitter.com/hseas http://harvardseasblog.blogspot.com http://digg.com/HarvardSEAS http://HarvardSEAS.tumblr.com

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fMRI time series in surface space
by Kushal Kapse 31 May '12

31 May '12

> Hi Everyone, > > I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation. > > My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space? > > Many thanks, > kk

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correlation coefficient
by Knut J Bjuland 31 May '12

31 May '12

Hi I am trying to calculate correlation coefficient using freesurfer GLM for associations between volumes and IQ. I found this ealier answar, but the matlab script but the link appear to be dead. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22648.html Best regards Knut J

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