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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

4 33

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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using own average subject
by Schuster, Christina /DZNE 31 May '12

31 May '12

Dear FreeSurfer experts, I am trying to create an average subject based on a matched subsample (2 different scanners, patients and healthy controls). I successfully ran make_average_subject receiving a "newtemplate". Now I am unsure how to proceed: As far as I understand it, according to the SurfaceRegAndTemplates page (http://surfer.nmr.mgh.harvard.edu//fswiki/SurfaceRegAndTemplates) I should use mris_register for each subject from my subsample receiving ?h.sphere.reg.newtemple files with which I should make again an average subject, let's call it "newnewtemplate". Is that correct? Now, if I want to assemble the data into common space using mris_preproc: what do I need to specify? Would --target be the newtemplate or newnewtemplate? Do I need to specifiy the --surf-reg as well? On the other hand, I read in one of your tutorials that I only need to run make_average_subject receiving a "newtemplate" which I then specify using mris_preproc as --target and that --surf-reg is not needed. So what would be the correct way to use my own template for the group analysis? Many thanks for you help! Best wishes Christina *********************** Christina Schuster, M.Sc. Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) Standort Rostock/ Greifswald Sitz am Zentrum für Nervenheilkunde (über Station N4) Gehlsheimer Straße 20 D- 18147 Rostock Tel: +49-381-494-9618 Fax: +49-381-494-9472 E-mail: christina.schuster(a)dzne.de Web: http://www.dzne.de *********************** Vorstand: Prof. Pierluigi Nicotera, MD PhD (Vorstandsvorsitzender und wissenschaftliches Vorstandsmitglied) und Ursula Weyrich (administratives Vorstandsmitglied) eingetragen in das Vereinsregister des Amtsgerichts Bonn (Az. VR 9021) ***********************

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Job advertisement
by Direktion, Institut f. Schlaganfall- und Demenzforschung 31 May '12

31 May '12

The Institute for Stroke and Dementia Research (ISD) is looking for a Post-doctoral Research Fellow: Imaging in Neurodegenerative Diseases RESPONSIBILITIES: The research fellow will acquire and analyze multimodal neuroimaging data on Alzheimer's disease, including structural and functional MRI, amyloid PET, and FDG-PET. The research project focuses on tracking structural and functional brain changes in preclinical Alzheimer's disease. The fellow will also have the opportunity to work on data from pre-existing data sets such as the Alzheimer's Disease Neuroimaging Initiative (ADNI) that will provide the basis for immediate data analysis and publications. REQUIREMENTS: The candidate should hold a PhD, MD or equivalent degree in relevant disciplines (informatics, engineering, mathematics, neuroscience). Skills in image registration and segmentation are desirable. Solid knowledge of programming and statistics is a plus. Familiarity with biological or clinical aspects of Alzheimer's disease is not a prerequisite. An enthusiastic, reliable and independent work style will provide a good fit for our team. OFFER: Our institute offers an excellent multidisciplinary environment (medical scientists, neuropsychologists, biologists, bioinformaticians, epidemiologists) with a powerful IT infrastructure and state-of-the-art scanners (3 & 7T MRI, molecular PET). The research fellow will have clearly defined task definitions, access to all data sets of the research project, and advanced technical support to facilitate efficient work conditions. The fellow will work in a friendly, dynamic, and highly productive team, headed by Prof. Michael Ewers, PhD. The University of Munich, Germany, and its clinics figure among Germany's premier and internationally competitive biomedical research sites funded by the government's German Universities Excellence Initiative. The Institute for Stroke and Dementia Research (ISD) is a thriving new research-dedicated institution (http://www.isd-muc.de) The ISD will be housed soon in a top-notch research facility that is currently being build and will eventually attract around 100 staff members, graduate students, scholars and foreign scholars. Salary is according to TV-L. The position is limited for two years, extension is desired. Disabled persons will be preferentially considered in case of equal qualification. Presentation costs can unfortunately not be refunded. For more information, please contact Mr. Frühauf, Tel.: +49 (0)89 7095 7800. HOW TO APPLY: Your application - preferably in electronic form - with the usual documents indicating the earliest possible starting date should be directed to: Klinikum der Universität München, Institute for Stroke and Dementia Research Markus A. Frühauf, Managing Director ISD Heiglhofstr. 55 81377 Munich | Germany E-Mail: isd(a)med.uni-muenchen.de

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long_qdec_table and LongQdecTable.py errors
by Jiyang Jiang 31 May '12

31 May '12

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

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Converting labels into .annot
by Sam Carpenter 30 May '12

30 May '12

Hi all, We have a series of labels (over 100) that encompass the majority of the cortex, but some minute vertices remained unlabeled. We've tried several attempts to make this .annot file and as well as attempts to label the unlabeled vertices (from a previous post 'labeling unlabeled vertices..'). But still to no avail. Question: how to convert .label files to .annot file, when some vertices are still unassigned. Thanks!!!

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Re: [Freesurfer] [martinos-tech] checking talairach registration
by Douglas N Greve 30 May '12

30 May '12

Hi Suzanne, it does not mean that there is anything wrong with your data. I've seen this before on some data sets. I have a work-around that might work. How many data sets do you have to run? doug On 05/29/2012 02:35 PM, suzanne oosterwijk wrote: > > Hi, > > Recently I ran recon1 for several participants. After recon1 I checked > the talairach transform with tkregister2. I noticed that for about 5 > out of 7 participants the original surface did not line up with the > fuzzy moveable volume. Specifically, the fuzzy volume was too small > for the green surface, in such a way that the green lines would > overlap with the skull, the dura or the eyes. I adjusted the > registration, mostly by scaling the brain. I think I was able to > realign everything correctly, but after checking with some colleagues > I heard that they never had this kind of trouble with the > registration. Is this normal? Or is this a sign that somewhere in the > pipeline (or during scanning) something went wrong? > > My data can be found at: > > /autofs/space/boggart_001/users/oosterwi/oosterwi_feedback/feedback_structural > > Thanks in advance for any comments/advice on this! > > Suzanne > > -- > > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Interdisciplinary Affective Science Lab > > Department of Psychology > > Northeastern University > > 114 Lake Hall > > Boston, United States > > s.oosterwijk(a)neu.edu <mailto:s.oosterwijk@neu.edu> > > https://sites.google.com/site/suzanneoosterwijk/ > > > __._,_.___ > Reply to sender > <mailto:suzanne.oosterwijk@gmail.com?subject=Re%3A%20checking%20talairach%20registration> > | Reply to group > <mailto:martinos-tech@yahoogroups.com?subject=Re%3A%20checking%20talairach%20registration> > | Reply via web post > <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJwNThjMnR2BF9TA…> > | Start a New Topic > <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJlNjZpM2V0BF9TA…> > > Messages in this topic > <http://groups.yahoo.com/group/martinos-tech/message/5666;_ylc=X3oDMTM0cGxvZ…> > (1) > Recent Activity: > > Visit Your Group > <http://groups.yahoo.com/group/martinos-tech;_ylc=X3oDMTJlZmFzYnBmBF9TAzk3Mz…> > > Yahoo! Groups > <http://groups.yahoo.com/;_ylc=X3oDMTJkanUycTR0BF9TAzk3NDc2NTkwBGdycElkAzQ5O…> > > Switch to: Text-Only > <mailto:martinos-tech-traditional@yahoogroups.com?subject=Change%20Delivery%20Format:%20Traditional>, > Daily Digest > <mailto:martinos-tech-digest@yahoogroups.com?subject=Email%20Delivery:%20Digest> > • Unsubscribe > <mailto:martinos-tech-unsubscribe@yahoogroups.com?subject=Unsubscribe> > • Terms of Use <http://docs.yahoo.com/info/terms/> > . > > __,_._,___ -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

2 1

mri_glmfit error
by YUMI MAEDA 30 May '12

30 May '12

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

1 0

subcortical segmentation
by Richter, Julia 30 May '12

30 May '12

Dear FreeSurfer experts, I have a question regarding the subcortical segmentation. In the paper by Fischl et al (2002), I've read that the neuroanatomical labels are assigned to the voxels based on probabilistic information automatically estimated from a manually labeled training set. I don't understand which atlas is used though. Is it an atlas of the Center for Morphometric Analysis? How shall I cite it? Thank you very much for your help in advance, Julia

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