Freesurfer January 2012

freesurfer@nmr.mgh.harvard.edu

97 participants
171 discussions

Too many levels of symbolic links
by cloud.ctrl＠me.com 27 Jan '12

27 Jan '12

I have subjects exiting with errors and I'm not sure why. The best clue I have is a line indicating "Too many levels of symbolic links" and an inability to read lh.BA1.label. Here are the last few lines of output: SUBJECTS_DIR /Applications/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer Loading source label. Too many levels of symbolic links ERROR reading /Applications/freesurfer/subjects/fsaverage/label/lh.BA1.label Darwin stat-240-26.sdsu.edu 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 recon-all -s GB exited with ERRORS at Thu Jan 26 00:29:32 PST 2012 Can anyone tell me what is happening here?

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how can I view and process Freesurfer files using AFNI
by Rashmi Singh 27 Jan '12

27 Jan '12

Hello, I ran recon all on my subjects data which went well. Now I would like to use AFNI-SUMA to view it , how do I go about doing this. Thanks, Rashmi. ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

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FreeSurfer download failed
by Browne, Aaron N 27 Jan '12

27 Jan '12

Hi! I would love to start using FreeSurfer and cannot download the software from your server. I am on a 32 bit GNU/Linux virtual machine running CentOS 5.7 and typed the following command: wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Linux… my output is: --2012-01-26 14:58:03-- ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Linux… => `freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz' Resolving surfer.nmr.mgh.harvard.edu... 132.183.202.158 Connecting to surfer.nmr.mgh.harvard.edu|132.183.202.158|:21... failed: Connection refused. I also tried clicking the download link in a firefox browser on my machine and got an "Unable to connect" error page. Did you move to a new server or something? Thanks for any help you can provide! Aaron Research Assistant Center for Autism Research The Children's Hospital of Philadelphia 3535 Market Street, Suite 860 Philadelphia, PA 19104 Phone: 267-426-4900 Fax: 267-426-7590 email: brownea(a)email.chop.edu<mailto:rileym1@email.chop.edu>

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Two FS versions in different user accounts
by _andreia_＠sapo.pt 27 Jan '12

27 Jan '12

Hi everyone, I'm sorry to bring this question up again, but I'm thinking to install version 5.1 in the same computer where version 5.0 is installed. However I'm thinking of installing the new one in another user account that I've created only for this porpuse. My question is, can I install and work in the new user independently? This way I won't need to be changing the subjects dir and the freesurfer environment each time I want to work with 5.0 or 5.1, right? Advice needed =) Thanks, Andreia

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Two FS versions in different user accounts
by _andreia_＠sapo.pt 27 Jan '12

27 Jan '12

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HandDrawn & Aseg amygdala comparisons.
by Jamie Hanson 26 Jan '12

26 Jan '12

Hi Freesurfer list- I was trying to compare hand-drawn amygdalae and amygdala volumes generated by mri_ca_label/aseg (similar to what Morey et al., 2009 did) and wanted some advice. My amygdalae are drawn by hand in pathological plane, with a quite labor intensive tracing routine. And I wondered the best way to get my aseg volumes into that (path plane) space (b/c I didn't want to move the hand-drawn masks)? Initially, I just aligned my raw T1w to pathological plane T1s and ran recon-all on these images, but the bivariate correlations between automated aseg volumes and hand-drawn amygdala dropped a fair amount (r=.5 in raw space, to r=.3 in path plane). I presume the re-alignment to path plane is adding some additional smoothing (which lowers mri_ca_label accuracy?). I didn't think it would be a fair comparison to calculate dice-coefficients, intersection/union, etc. with aseg pathological plane amygdala (compared to my hand-drawn amygdala). Is the best practice to segment in original space, calculate the transform on the T1 from orig to path-plane, and then apply that transformation matrix to the aseg volume generated from the raw T1? Are there other suggestions? Any advice is greatly appreciated! Thanks much! Best, jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53705 Email: jamielarshanson(a)gmail.com Homepage: http://brainimaging.waisman.wisc.edu/~hanson/

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write dipoles function
by Guthormsen, Amy M 26 Jan '12

26 Jan '12

Hello, I would like to try out the Tools-->surface-->write dipoles function, but I don't know how to read the file that it outputs. Do I need to use a special file extension when I name the file? Thank you, Amy

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22-30 June 2012: 10th IEEE EMBS International Summer School on Biomedical Imaging (fwd)
by Lilla Zollei 26 Jan '12

26 Jan '12

Hi, Could you forward the below to interested students / collaborators? I attended this summer school both as a student and as a lecturer in the past and I can highly reccomend it. --Lilla ------------------------------------------------------------------------ CALL FOR PARTICIPATION (APOLOGIES FOR MULTIPLE COPIES) 10th IEEE EMBS International Summer School on Biomedical Imaging 22-30 June 2012 Berder Island, France WEB http://ieeess.enst-bretagne.fr Application deadline : Feb. 15, 2012 E-mail : Valerie.Burdin(a)telecom-bretagne.eu Chair : Christian ROUX Co-chair : Jean-Louis COATRIEUX The spirit of this Summer School is inspired by the most prestigious school ever founded in France, Saint Flour, the influence of which has spread to generations of researchers in Mathematics. Since its establishment in Brittany in 1994, this school has become a worldwide reference. It is resolutely international (participants from more than twenty countries have participated to the previous editions) and accessible to young scientists. It is an open yet privileged place for exchanges and discussions of major on-going work. Informal and warm, at a location where the sea and the land combine in a time varying relation, this school brings together, every two years for ten days, the world great teachers and researchers in Biomedical Imaging. Lectures, seminars, and discussions are organized at the highest level, but with the freedom of spirit that is the tradition of Brittany. The school objective is to contribute without any exclusion to advances in a rapidly evolving field, and to foster participation in the adventure of research. It provides up-to-date, state-of-art knowledge on emerging areas and addresses important issues dealing with complex, multivariate systems, going from basic to applied research. Audience: The Summer School is open to graduate students (M.S., PhD), post doctoral scientists, radiologists, biologists, researchers and engineers in industry. 2012 Program SIMON CHERRY, University of California Davis, USA, “Molecular Imaging” RUSS TAYLOR, Johns Hopkins University, USA “Computer-Integrated Surgery” MICHAEL UNSER, Ecole Polytechnique Fédérale de Lausanne, Switzerland “Biomedical Image Analysis” SIMON ARRIDGE, University College London, UK “Optical Tomography” KOJI IKUTA, University of Tokyo, Japan “Nano Robots for Cell Investigation” JEAN YVES CHAPELON, INSERM, Lyon, France,“Therapeutic Ultrasound” Junior Lecturer It is now an established tradition to invite the participants of the previous schools (2004, 2006, 2008and 2010) to serve as Junior Lecturer for the next one (2012). An international Committee will select the junior lecturer. The topics that can be addressed by this Junior Lecture are very open, as far as they concern Biomedical Imaging. The talk to be given is expected to complement the lectures already displayed. Experience and originality of the subject, interest for the audience are the basic criteria to fulfill. Travelling expenses lodging and fees will be paid. http://ieeess.enst-bretagne.fr/index.php?pid=8 Call for Participation The number of attendees (traditionally coming from more than 30 countries all over the world) is strictly limited (45) and applications must be submitted as early as possible (the formal deadline being February 15, 2012). An international committee will select the candidates by March 15. Participants are encouraged to present their research work through Posters. http://ieeess.enst-bretagne.fr/index.php?pid=3 Candidature submission is open from Nov. 15, 2011 to Feb. 15, 2012 For information contact : Valérie Burdin, Département ITI, TELECOM Bretagne, CS 83818, 29238 Brest Cedex 3, France E-mail : Valerie.Burdin(a)telecom-bretagne.eu

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hippocampal subfields segmentation
by JOANA BRAGA PEREIRA 26 Jan '12

26 Jan '12

Dear Koen & Freesurfers, I've been working with the GEMS tool for hippocampal subfields segmentation and have a question I would like to ask you all. I've noticed that the CA1 sector appears to be quite small compared to other subfields (CA2-3 seems to be the largest), while previous studies suggest that it should be the largest subfield of the hippocampus. Why? On the other hand, I have read the paper by Van Leemput et al. [2009] and how the subfields were initially delineated and was wondering what atlas was the manual tracing based on? Many thanks! joana

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overlay alignment in tkmedit
by Anthony Dick 26 Jan '12

26 Jan '12

Hello, I am trying to train a cerebellar atlas based on 20 manually parcellated cerebellums. I have run the anatomical through freesurfer. When I try to load the overlay (parcellation) in tkmedit, the underlay (e.g., orig.mgz, T1.mgz) and the overlay (the parcellation) are no longer in alignment. However, loaded in AFNI the underlay and overlay of course align. Is there a quick fix to get them in alignment? Anthony -- Anthony Steven Dick, Ph.D. Assistant Professor Department of Psychology Florida International University Modesto A. Maidique Campus DM 296B 11200 S.W. 8th Street Miami, FL 33199 Phone: 305-348-4202 (try this first) Lab Phone: 305-348-9057 or 305-348-9055 Fax: 305-348-3879 Email: adick(a)fiu.edu Webpage: http://www.fiu.edu/~adick

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Freesurfer January 2012