Freesurfer June 2008

freesurfer@nmr.mgh.harvard.edu

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Tutorial Example Data
by Yuan Xu 26 Jun '08

26 Jun '08

2 1

brainmask.mgz vs. brain.mgz
by p.s.bjerkan＠studmed.uio.no 26 Jun '08

26 Jun '08

Hi! Have a couple of questions regarding manual edits correcting the pial-surface. Have found out, in some of our data sets, that the brain.mgz file has been used instead of the brainmask.mgz during edits to correct the pial surface. Seems that this protocol has been inherited from pre-version 3.0 work-ups. Therefore; 1) What does this imply for the data? Generally, when we have inspected the surfaces after recon2 is rerun it seems that the corrections are taken into account. Have tried to analyze the process stream in order to localize what the implications would be, but I am not sure I understand it. 2) What should we do when we have more data in the same study that is not controlled yet, keep on doing the same thing or switch? Yours sincerely, Petr Szulc Bjerkan Dept. of psychiatry University of Oslo

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GTCA
by Daniel H Choi 26 Jun '08

26 Jun '08

Does anyone know if GTCA is part of the freesurfer commands? My protocol requires that I use a "GTCA" command to create a better surface image for stg. If not, can anyone direct me towards a resource to explain what it is and how to use it? Thanks. -- Daniel Horim Choi Northwestern University Class of 2009 dhchoi(a)u.northwestern.edu or dchoi1024(a)gmail.com

1 0

significance thresholds and multiple comparisons corrections
by Judith Segall 26 Jun '08

26 Jun '08

Hi FreeSurfer groupers. I have been using FreeSurfer since v3.0.2, but still have some questions about the group analysis pipelines. I have used both QDEC and the previous manual method using glm_fit. Questions about QDEC: 1. What are the guidelines for setting significance thresholds, by adjusting the color thresholds? 2. Should the FDR correction for multiple comparisons that is is the GUI be used? Previously, we used mri_glmfit to correct for multiple comparisons, using the mc-z-z- monte carlo simulation method. We would then report the p-values obtained from the clustering. My main question is what is the best direction to take after using QDEC, i.e. how to correct for multiple comparisons? Also, are there any advantages/disadvantages to using QDEC/glm_fit, for example circumstances where one would be better to use. (For instance, you can have more factors when using glm_fit) I appreciate any help or suggestions that anyone has to give, for I am trying to finish two papers using freesurfer. Also, thanks for developing QDEC, for it makes second level analysis easier to set up. Thanks, - Judith S.

1 0

segmentation protocol for the hippocampus
by Nicolas Cherbuin 26 Jun '08

26 Jun '08

Hi, Where can I find the protocol used to segment the hippocampus in freesurfer? I am comparing manually traced hippocampi to fs segmentation and I am interested to know whether differences are due to the protocol used or other factors. Thanks Regards, Nic Nicolas Cherbuin Research Fellow Centre for Mental Health Research Australian National University Canberra ACT 0200 Ph: 61 2 61253858 Fax: 61 2 61250733 Email: nicolas.cherbuin(a)anu.edu.au CRICOS Provider # 00120C

3 2

atlas renormalization
by Juranek, Jenifer 26 Jun '08

26 Jun '08

Another curious question: The atlas renormalization process described by Han & Fischl (2007)...which version of freesurfer was this introduced? Many Thanks, Jenifer

1 1

Technical Assistant Position at MIT
by David Ziegler 25 Jun '08

25 Jun '08

The Behavioral Neuroscience Laboratory, led by Dr. Suzanne Corkin in the Department of Brain and Cognitive Sciences at MIT, is seeking a highly motivated person to join a laboratory examining the changes in brain structure and cognition that occur in healthy aging and age-related degenerative disease. The successful candidate will participate in all aspects of neuroimaging research, including study design, participant recruitment and screening, data acquisition and processing, statistical analysis, and publication; and have primary responsibility for lab computer systems, networks, and data storage. This position is ideal for those considering future graduate or medical studies. REQUIREMENTS: strong organizational skills and proficiency with programming/scripting (e.g., MATLAB, Python, csh/tcsh/bash) and Linux/UNIX operating systems. Demonstrated interest and/or experience in neuroscience preferred, as is familiarity with Mac OS X systems and end-user computer support. Should be comfortable working with research participants of all ages, including patients with neurodegenerative disease. Must be able to obtain certification to operate critical research equipment (MRI/MEG scanners). A one-year commitment is requested, with a possibility for continued employment thereafter. In addition to a resume/CV, application material should include a cover letter and the names of three references. To apply, please upload a resume and cover letter via the following link: http://sh.webhire.com/servlet/av/jd?ai=631&ji=2224764&sn=I -- David A. Ziegler Department of Brain and Cognitive Sciences Massachusetts Institute of Technology 43 Vassar St, 46-5121 Cambridge, MA 02139 Tel: 617-258-0765 Fax: 617-253-1504 daz(a)mit.edu <mailto:daz@mit.edu>

1 0

monkey template
by Jan Kalkus 25 Jun '08

25 Jun '08

Hi, I'm trying to construct a surface registration template with some monkey data and I was wondering if anyone could clear up some confusion I had. Can anyone tell me what the difference between mri_make_template and mris_make_template is? Thanks, Jan Kalkus

1 0

how to continue from breaking point of 'recon-all'
by Woo-Suk, Tae 25 Jun '08

25 Jun '08

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; } Dear Freesurfer expertsMy one 'recon-all -all' process was terminated with a library error.So I'd like to continue the rest process after library update.How can do it? Woo-Suk, TaeChuncheon, Korea

2 1

dicom to mgz
by Daniel H Choi 24 Jun '08

24 Jun '08

Hi, I was wondering if there was a way to change all of the dicom files from one brain to one .mgz file. Thanks Dan -- Daniel Horim Choi Northwestern University dhchoi(a)u.northwestern.edu or dchoi1024(a)gmail.com

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Freesurfer June 2008