Freesurfer July 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
140 discussions

subcortical segmentation
by Hannoun 07 Jul '10

07 Jul '10

Hi, I am a new user of freesurfer. Is it possible to do just the volumetric processing stages without the surface processing stages? In fact what I want is to segment the subcortical structures. Is there a command line for this purpose only or should we run all the recon-all steps? Thank you for your help Salem

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surface-based cytoarchitectonic map
by Danny Kim 06 Jul '10

06 Jul '10

Hi Freesurfer users, In the paper, "Cortical folding patterns and predicting cytoarchitecture" by Fischl et al (Cerebral Cortex, 2008), it's mentioned that "surface-based probabilistic maps of the cytoarchitectonics can be downloaded from http://surfer.nmr.mgh.harvard.edu/fswiki". I can't seem to find them there in the wiki.. anyone know where they might be? Thank you Best Regards, Danny Kim Brainmapping BC Children's Hospital

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Spatial info of vertices
by Dankner, Nathan (NIH/NIMH) [F] 06 Jul '10

06 Jul '10

Hi all, I'm hoping to extract the connections and distances (edge and weight) of the vertices for each of my individual subjects' surfaces. How can I go about doing this? Thanks! Nathan

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Post-doctoral Position in Vascular Dementia Research at the German Center for Neurodegenerative Diseases (DZNE) in Munich
by Graf, Christina /DZNE 06 Jul '10

06 Jul '10

Post-doctoral Position in Vascular Dementia Research at the German Center for Neurodegenerative Diseases (DZNE) in Munich The German Centre for Neurodegenerative Diseases (www.dzne.de<http://www.dzne.de/>) has been newly founded by the Helmholtz Foundation. The DZNE Munich is now offering a post-doctoral Position in Vascular Dementia Research. The mission of the DZNE is to investigate neurodegenerative diseases of the ageing human brain, in particular Alzheimer's and Parkinson's disease, while also studying interactions with other neurological disorders relevant to ageing and dementia. A joint project between three different sites of the DZNE will focus on mechanisms of vascular and mixed dementia. For a project on the neural correlates of cognitive and behavioral dysfunction in vascular cognitive impairment the DZNE Munich in collaboration with Institute for Stroke and Dementia Research (www.isd-muc.de<http://www.isd-muc.de/>) is searching for a scientist with a background in cognitive neuroscience and image post-processing. The candidate must have attained a PhD or MD degree and should have skills in the following areas: MR image post-processing (FSL, SPM, Matlab etc.); statistics, programming (optional), neuropsychology (optional). The Institute for Stroke and Dementia Research (ISD) / DZNE Munich closely collaborates with national and international partners thus providing a stimulating environment for highly motivated and creative scientists. The position is for 3 years and will be opened in September 2010. Employment, payment and social benefits are determined by the Public Sector Collective Agreement (Tarifvertrag für den öffentlichen Dienst - TVöD). The DZNE seeks to increase the number of female personnel in those areas where they are underrepresented and therefore explicitly encourages women to apply. The DZNE is committed to employing more disabled individuals and especially encourages them to apply. Applications including a CV, a list of publications and a research summary should be sent electronically to isd(at)med.uni-muenchen.de<mailto:isd@med.uni-muenchen.de>. The application deadline will be July, 31 2010 time limit: 31.07.2010 place: Munich contact: Prof. Martin Dichgans (isd(at)med.uni-muenchen.de<mailto:isd@med.uni-muenchen.de>) Kind regards Christina Graf Personal und Organisation * Human Resources Department Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)

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Watershed Errors - Multiple attempts tried
by Christian Lambert 06 Jul '10

06 Jul '10

Hi all, I'm assissting with an aging study and a good handful of their scans are coming up with watershed errors. My assumption was errors with the skull strip leading to empty brain volumes. I have read through all the lists and tried the following: - Manually corgistering to MNI to improve Talairich alignment; Same error - Using a range of -wsthresh (from 30-55) with the -no-wsgcaatlas -wsthresh command in recon all; these all had very bad skull strips but avoided watershed error. They all crashed later on at register_mri: find_optimal_transform - Rescaling the voxel intesity ranges to be closer to "successful" scans (watershed error again) I'm not entirely sure what to try next. I'm using Magnetic Transfer Images that I've multiplied the voxel intesities by 1000 (as normally 0.6-1.5) in order to freesurefer (which works well in most subjects). Other images I have available are T1, T1w, PDw,MTw. I'm avoiding the weighted scans due to coil induced bias. I have tried the T1 with identical results. WM values=~1800-1900 GM Values= 900 CSF = 50 Out of brain ~300 Cheers for any help you can provide, - Chris

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Regression analysis on files produced with the -osgm flag
by Jürgen Hänggi 06 Jul '10

06 Jul '10

Dear FS experts We have done a one-sample-group-mean (osgm) analysis and now we would like correlate a behavioural measure with the difference maps produced by the -osgm analysis. Is this possible? Or do we have to compute the difference of each subject again, the running mri_surf2surf to register the difference files and then running the regression? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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position announcement: Research Program Coordinator/MRI Data Analyst
by Julie E McEntee 05 Jul '10

05 Jul '10

The Division of Psychiatric Neuroimaging in the Department of Psychiatry, Johns Hopkins University School of Medicine (Baltimore, MD), is seeking a Research Program Coordinator/MRI Data Analyst. The position will oversee all facets of research activities, data management and administrative aspects for research projects involving multimodal imaging (structural, fMRI, DTI, MRS) on the 3 T and 7 T Philips systems at the F. M. Kirby Center for Functional Neuroimaging, imaging systems at JHH, or other imaging systems. Current research projects include studies of Huntington’s Disease, schizophrenia, anorexia nervosa, other neuropsychiatric conditions and healthy control populations. The primary duties and responsibilities include: Assist development of fMRI neuropsychological protocols, recruit and enroll participants, administer clinical neuropsychological tests and research tasks, assist (with MRI technician) in image acquisition, enter research data, conduct data and image analysis. Essential job functions: Maintaining and monitoring supply of testing materials, monitoring the control of data quality and research integrity. The duties also include organizing and maintaining research files and maintaining study databases. Responsible for the development of IRB applications as well as IRB compliance. Master’s degree in psychology, neuroscience or related discipline relevant to imaging is strongly preferred. Advanced experience with personal computers, Windows 7 and Mac OS operating systems and Microsoft Office 2007/2010 applications (particularly Excel and Access) required; experience with UNIX preferred. Knowledge of univariate and multivariate statistics required; experience with statistical analysis software (e.g., SPSS, SAS, Stata) preferred. Knowledge of imaging analysis software (e.g., SPM, FSL, AFNI, FreeSurfer, MIPAV) preferred. Clinical research experience with neuropsychiatric populations and database management required; experience with completing Case Report Forms (CRF’s) and creating source documents a plus. Must be extremely well organized, precise and detail oriented. Must have the excellent interpersonal skills, ability to problem solve and work independently. Please send statement of interest and CV to Julie McEntee at jmcentee(a)jhmi.edu and Graham Redgrave at gwr(a)jhmi.edu. Julie E. McEntee, M.A., C.C.R.P. Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./ Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676

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Postdoctoral Fellowship - Neuroimaging of Langauge
by Rutvik Desai 05 Jul '10

05 Jul '10

A postdoctoral fellowship is available immediately at the Medical College of Wisconsin, Milwaukee, in the laboratory of Dr. Rutvik Desai, which is affiliated with the Language Imaging Laboratory (www.neuro.mcw.edu<https://owamail.mcw.edu/owa/redir.aspx?C=3b718d6eb18f4a7ead52886096b52157&U…>). The research in our lab focuses on language and speech processing. The NIH-funded project will emphasize semantics and embodiment of meaning, using neuroimaging techniques and patient studies. Close collaborators include Drs. Jeffrey Binder, Einat Liebenthal, Sylvain Baillet (MCW), Mark Seidenberg ,and Tim Rogers (UW Madison). State-of-the-art facilities include two 3T scanners, MEG, TMS, and EEG systems. A Ph.D. or equivalent in neuroscience, psychology, or a related field is required. Experience with language research using neuroimaging, TMS, computational modeling, or machine learning is highly desirable. The fellow will have an exciting opportunity to receive training, depending on their interest, in fMRI, TMS, MEG, EEG, and/or in conducting patient studies, and to pursue collaborative and self-directed projects. MCW has been ranked consistently as one of the “Best Places to Work” for postdoctoral fellows. Please email a CV, a statement of research background and interests, contacts of three references, and copies of relevant publications to Dr. Rutvik Desai at rhdesai(a)mcw.edu<https://owamail.mcw.edu/owa/redir.aspx?C=3b718d6eb18f4a7ead52886096b52157&U…> .

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How can I make aparc.2009 from aparc.2005
by Shahin 02 Jul '10

02 Jul '10

Hi everyone For my old subjects I already have aparc.2005 atlas file in the label directory but not the 2009a version. I want to know how can I make 2009 version for these subjects without doing the recon-all for them. Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard University

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Skullstrip Delay
by Riskin-Jones, Hannah 02 Jul '10

02 Jul '10

Hi, I am attempting to run an fMRI data set through the freesurfer workflow and the skullstripping step seems to be delayed. It has been stuck on the following command line for an inordinate amount of time. First Search limited to translation only. using real data threshold=28.0 Found translation: (-1.1, -8.0, -23.9): log p = -22300.7 Nine Parameter search. iteration 0 nscales = 0 ... without an error message, I have no clues as to how to fix this problem. Any suggestions would be much appreciated! Thank you so much, Hannah

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Freesurfer July 2010