Freesurfer

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PostDoc Positions at UCSD MultiModal Imaging Laboratory (MMIL)
by Don Hagler 29 Oct '09

29 Oct '09

Postdoctoral Research Scholar Position, Multimodal Imaging Laboratory, University of California, San Diego The Multimodal Imaging Laboratory (MMIL) at the University of California, San Diego invites applications for multiple postdoctoral research scholar positions under the direction of Dr. Anders Dale. The successful candidates will join a multi-disciplinary team of scientists, programmers, and support staff addressing a variety of neuroscience questions using multimodal brain imaging, electrophysiology, behavior, and genetics. An important component of the work done at MMIL, and the primary role for the currently announced positions, is the development and improvement of methods for the analysis of neuroimaging data. Postdoctoral researchers will receive training in brain imaging and methods development, and will be encouraged to develop their own research projects. The primary areas of development will include: 1. Segmentation of pediatric brain scans 2. Tractography and diffusion MRI analysis and modeling 3. Multispectral lesion segmentation and quantification 4. Longitudinal registration & analysis of contrast change 5. EEG/MEG/fMRI integration and modeling 6. Resting state fMRI & ASL analysis, quantification within anatomically-defined ROIs 7. Validation of non-invasive imaging measures using ex vivo histology and stereology Applicants for the position must have completed relevant Ph.D. research activities within the past five years. Applications from many disciplines may be considered, and the position is open to qualified international applicants. Experience or expertise in the following areas is highly desired: 1. computer programming experience (MATLAB, C/C++, Python, OpenGL, tcl/tk) 2. neuroimaging analysis methods (especially FreeSurfer) 3. structural MRI, DTI, fMRI, ASL 4. MRI physics and/or pulse programming 5. scientific writing This posting is for 2-year appointments beginning immediately. Salary will be consistent with the NIH/NRSA levels in accordance with the University of California, San Diego policies for Postdoctoral trainees. Compensation includes full staff benefits, including health insurance, and vacation time. Review of applications will begin immediately and will continue until the position is filled. To apply, please send your CV, a brief statement of research interests and goals, and any selected reprints to amdale(a)ucsd.edu with the subject line "MMIL postdoctoral position". Letters of reference will be required before final approval of hiring. Informal inquiries for more details are welcome. _________________________________________________________________ New Windows 7: Find the right PC for you. Learn more. http://www.microsoft.com/windows/pc-scout/default.aspx?CBID=wl&ocid=PID2472…

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effect of the radius on lGI
by Zhangyuanchao 29 Oct '09

29 Oct '09

Hi, expert, Could anyone tell me the effect of the radius on lGI. After reading the paper on lGI carefully, I still can not get a clear view of the effect of the radius on lGI. I still wonder why the default radius are chosen to be 25mm since there is very little discussion of the standard in choosing such a radius in the paper on TMI. When making group analysis, does the result vary greatly using different radii? and why is that? How to intepret the result obtained using different radii? Thank a lot! Best Regards ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

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GLM question
by Mehul Sampat 29 Oct '09

29 Oct '09

Hi FS folks, I have a basic GLM question. I went through the tutorials online but I was not sure and wanted to check with someone. I am trying to compare the cortical thickness between a group of patients (n = 166) and controls (n = 76). For patients mean age is 49.8 +/- 9.1 and there are 55 Male; 111 Female For controls mean age is 40.5 +/- 11.4 and there are 26 Male; 50 Female If include gender as a fixed factor does the output of the GLM answer the following: 1. "Is the cortical thickness different between the patients and controls accounting for gender" 2. As I understand the GLM setup one can control for gender and other discrete factors but not for continuous co-variates such as age ? That is one can find the association between thickness and age and see if it is different for the two groups. However if the age distributions for the two groups are different one cannot control for it with GLM. is this interpretation correct ? If so, how would one control for age in such an analysis ? Any help is much appreciated. Thanks Mehul 2. For the correction of multiple comparisons, when should one use FDR as compared to monte-carlo simulations ? Thanks Mehul

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WM hypointensities in aseg vs wmparc
by Dankner, Nathan (NIH/NIMH) [F] 29 Oct '09

29 Oct '09

Hello all, I was curious as to whether it is preferable to use the wm hypointensities output from wmparc.stats or from aseg.stats or if there is no real difference. Also, I believe I've seen this answered elsewhere, but just to be clear, is it the case that there is currently no way to visualize/label these in tkmedit?

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Re: [Freesurfer] Recon-all exited with ERRORS
by Angie Morales 29 Oct '09

29 Oct '09

Hi, I'm trying to run the command: recon-all -subjid <subname> -autorecon1. I'm getting the an error message during skull stripping and the error log reads as follows: #@# Skull Stripping Wed Oct 28 12:29:47 PDT 2009 /space/raid7/data/london/data/ mri/other/angie/Freesurfer/SUBJECTS_DIR/5003/mri mri_em_register -skull nu.mgz /space/raid/fmri/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/space/raid/fmri/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=14.0 skull bounding box = (51, 40, 26) --> (206, 255, 255) using (103, 112, 141) as brain centroid... mean wm in atlas = 126, using box (84,85,113) --> (122, 138,169) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 110, scaling input intensities by 1.145 scaling channel 0 by 1.14545 initial log_p = -19541.4 ************************************************ First Search limited to translation only. ************************************************ using real data threshold=42.0 Found translation: (-1.1, 1.1, -17.0): log p = -17915.1 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Linux willis 2.6.27.25-0.1-default #1 SMP 2009-07-01 15:37:09 +0200 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Oct 28 14:45:19 PDT 2009 The error log simply states: CMD mri_watershed Any advice on how to troubleshoot this problem would be greatly appreciated. Angie

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building from source
by Michael Scheel 29 Oct '09

29 Oct '09

Hi everybody, I have the opportunity to run my analysis with freesurfer on a big computer-cluster that is running on AIX. However to install freesurfer there I need to build it from source. Is the source code available? I found some older entries in the archives and the issue seemed at that time rather complicated. Are there any news regarding building from source? Thanks, Michael

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question about load_segstats
by Mehul Sampat 29 Oct '09

29 Oct '09

Hi FS folks I was trying to use the load_segstats function to read aseg.stats and wmparc.stats It works well will these files but I get the following error if I try to read lh.aparc.stats or rh.aparc.stats [segname segindex segstats] = load_segstats('lh.aparc.stats','bert'); ??? Subscripted assignment dimension mismatch. Error in ==> load_segstats at 113 segstats(nthrow,:) = [nvox vol segmn segstd segmin segmax segrng]; Any suggestions on how I could fix the matlab function ? Thanks Mehul

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Statistical output
by mmoayedi＠uhnres.utoronto.ca 29 Oct '09

29 Oct '09

Hi everyone, I was hoping you can clarify something for me. I'm comparing two groups using CTA (in freesurfer). When I set up my model, I include age as a covariate of no interest. To do this, I include it as a variable in the fsgd, and in the contrast matrix, I regress out the effects of age, by setting the vectors to 0. However, when I extract the results from the analysis (the thickness values), and graph them against age, I find that I have an interaction, or an age effect nonetheless. Could you please shed some light on this for me? Thanks, Massih

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problem starting qdec
by Dana W. Moore 29 Oct '09

29 Oct '09

Hi everyone, I am trying to use qdec for the first time, and I get the following error message: X Error of failed request: GLXBadRenderRequest Major opcode of failed request: 132 (GLX) Minor opcode of failed request: 1 (X_GLXRender) Serial number of failed request: 1705 Current serial number in output stream: 1709 Locking assertion failure. Backtrace: #0 /usr/lib/libxcb-xlib.so.0 [0x4455a767] #1 /usr/lib/libxcb-xlib.so.0(xcb_xlib_lock+0x2e) [0x4455a81e] #2 /usr/lib/libX11.so.6 [0x4033d518] #3 /usr/lib/libX11.so.6(XESetCloseDisplay+0x31) [0x403208d1] #4 /usr/lib/libGL.so.1 [0x40291b69] I am accessing our linux computer remotely using ssh from a windows machine--I don't know if this is related to the problem. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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Surface errors
by Evert van Velsen 29 Oct '09

29 Oct '09

Hi, I am trying to reconstruct the surfaces of 1.5T images that I have (n>800). In almost half of my images, minor portions of the temporal and orbitofrontal lobes are missing (e.g. see images attached). Has somebody any suggestions how to solve this problem in an easy way (FreeSurfer settings e.g.), as it is (almost) impossible to add control points for all subjects. Thanks, Evert

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