Freesurfer May 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

Difficulties in processing cortical thickness with 2 atrophic brains
by Zixuan Yang 03 May '12

03 May '12

Dear Freesurfer experts, I am processing some atrophic brains with Freesurfer. However considerable part of 2 participants' brains (WM+GM) is not recognized (especially for participant B, the posterior part is not processed at all). I have checked the Talairach registration of both, only the borderlines of the posterior brain regions are not exactly accurate. Then I have tried to add thousands of control points and run the <recon-all -autorecon2-cp -s subject name> but that doesn't help. Please find the attached slides of 2 participants. Could you please give me some suggestions for better processing or further editing? Many thanks!! Kind regards, Zixuan -- Zixuan YANG Ph.D student UNSW School of Psychiatry NPI - Euroa Centre, Prince of Wales Hospital Barker Street, RANDWICK NSW 2031 Australia Tel: 0405256313 Email: zixuan.yang1(a)unsw.edu.au<mailto:zixuan.yang1@unsw.edu.au>

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recon-all error
by bowang21＠mail.ustc.edu.cn 03 May '12

03 May '12

Dear FreeSurfer experts, I have 20 subjects' data to analysis.And I started 20 terminals to process each subject's data.But they come across error one by one.By now there have been 17 subjects' processes stoped. By the way, I use virtualBOX whose RAM are 4G to process the data.I wander if there are some conflicts when proecess many datas in the meantime? In the adjunct,there are some errors reported by Freesurfer. Yours Bobo

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Vertex wise analysis and area/pial area/volume interpretation
by Mahinda Yogarajah 03 May '12

03 May '12

Dear Experts, I had 2 questions with regard to vertex wise analysis using qdec. 1) How should one interpret the dependent variables area/pial area and volume when comparing 2 groups with qdec and a vertex wise (as opposed to ROI based) analysis - or are they uninterpretable in this context ? I read briefly about areal as an alternative measure - could someone explain the difference, and how thickness, volume and area related to one another ? 2) When running monte-carlo cluster wise multiple correction in qdec - if one finds a significant cluster is it ok to view them within qdec by highlighting the "mc-z ... " file in the analysis result box, and then changing the minimum threshold to whatever value one selected for the monte carlo simulation ? The reason I ask is that the text ouput given by the monte carlo cluster analysis gives different coorinates in the cluster table to that output given when one clicks on the "find clusters and go to max" button ... Thanks. Mahinda

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asegstats2table problem
by Brain Apprentice 03 May '12

03 May '12

Hello Surfers, Command: asegstats2table --skip --delimiter comma --common-segs --stats=lh.BA.stats --meas volume --tablefile V5vo-BA-lh.csv --subjectsfile=a.txt I am trying to create a table of "lh.BA.stats" values where all subject are listed in a.txt. asegstats2table tries to work however there is nothing in the table but the subject-id's. Does anyone have any ideas what is going wrong? Thanks, B.A.

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.Licence file
by U. Anazodo 03 May '12

03 May '12

Hello, I downloaded and installed freesurfer with the instructions outlined from the Freesurfer wiki. I am using Ubuntu 10.4. I registered and got an email that directed me to copy and past three lines to a '.licence file' in the $FREESURFER_HOME (which in my case is /usr/local/freesurfer). But I can't locate the '.licence' file in the folder? is the file in the folder or is it something I have to create?? thanks. Oh I checked the freesurfer mailing list seems to be a problem but the solution is not stated clearly. Thanks. Udunna

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Atlas issues
by farras abdelnour 03 May '12

03 May '12

Dear FreeSurfer experts, I am in Charlestown for a short course at MGH until tomorrow, Friday, 4PM. I have a couple of questions on how to incorporate an atlas for a population of subjects under 5 year-old into FreeSurfer. I would greatly appreciate it if I can meet with a FreeSurfer sometime tomorrow, Friday. With thanks. -- Farras Abdelnour farras.abdelnour(a)gmail.com http://pittsburgh.academia.edu/FarrasAbdelnour

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Re: [Freesurfer] surfaceRAS to Talairach
by Jordan Poppenk 03 May '12

03 May '12

Dear Douglas, That's exactly the information I was looking for. This worked perfectly. Thank you for your help! Cheers, Jordan > Here's how to convert from surface RAS to mni305 > > mni305ras = X*S*inv(K)*ras > X = talairach.xfm > S = scanner vox2ras (mri_info --vox2ras orig.mgz) > K = tkreg vox2ras (mri_info --vox2ras-tkr orig.mgz) > ras = surface ras > > If you want to go from mni305 to approximate talairach, you can use this > transform from Matthew Brett: > > > function outpoints = mni2tal(inpoints) > % Converts coordinates from MNI brain to best guess > % for equivalent Talairach coordinates > % FORMAT outpoints = mni2tal(inpoints) > % Where inpoints is N by 3 or 3 by N matrix of coordinates > % (N being the number of points) > % outpoints is the coordinate matrix with Talairach points > % Matthew Brett 10/8/99 > > dimdim = find(size(inpoints) == 3); > if isempty(dimdim) > error('input must be a N by 3 or 3 by N matrix') > end > if dimdim == 2 > inpoints = inpoints'; %' > end > > % Transformation matrices, different zooms above/below AC > upT = spm_matrix([0 0 0 0.05 0 0 0.99 0.97 0.92]); > downT = spm_matrix([0 0 0 0.05 0 0 0.99 0.97 0.84]); > > tmp = inpoints(3,:)<0; % 1 if below AC > inpoints = [inpoints; ones(1, size(inpoints, 2))]; > inpoints(:, tmp) = downT * inpoints(:, tmp); > inpoints(:, ~tmp) = upT * inpoints(:, ~tmp); > outpoints = inpoints(1:3, :); > if dimdim == 2 > outpoints = outpoints'; %' > end > > > > > > > On 05/02/2012 12:54 PM, Jordan Poppenk wrote: > > > Dear FreeSurfer experts, > > > > > > How does one properly convert from surfaceRAS coords, as provided by fs_read_surf.m, to talairach coords? I have tried using freesurfer_surf2tal.m posted on the web by Darren Weber, supplying it with transform data from transforms/talairach.xfm, but the values returned often differ from those in tksurfer by as much as 20mm (and are clearly wrong). What I would like to do is match the coordinate system in tksurfer (which is clearly right). How does tksurfer do it? > > > > > > Cheers, > > > > Jordan > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > Freesurfer at nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > > greve at 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

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not all taskreg in design matrix
by Caspar M. Schwiedrzik 03 May '12

03 May '12

Hi, I am trying to use mkanalysis-sess in version 5.1 with 5 external regressors. I have prepared them as individual text files. When I run mkanalysis-sess -force -notask -a lot of other stuff -taskreg seed1 1 -taskreg seed2 1 -taskreg seed3 1 -taskreg seed4 1 -taskreg seed5 1 -nuisreg global.waveform.dat 1 -mcextreg followed by slxavg3-sess, I only get contrasts for seeds 1-4. Seed 5 is apparently not in the design matrix. Is there a limit to the number of external regressors? I guess I could circumvent this by having one text file with all five regressors, correct? Thanks, Caspar

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Faculty openings in Integrated Imaging at Purdue University (fwd)
by Bruce Fischl 03 May '12

03 May '12

FYI ---------- Forwarded message ---------- Date: Thu, 3 May 2012 14:23:46 -0400 From: Thomas Talavage <tmt(a)purdue.edu> To: "Bandettini, Peter (NIH/NIMH) [E]" <bandettp(a)mail.nih.gov>, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>, Douglas C. Noll <dnoll(a)umich.edu>, Steve Wright <smwright(a)tamu.edu>, "Buxton, Richard" <rbuxton(a)ucsd.edu>, Noam Harel <noam(a)cmrr.umn.edu> Subject: Faculty openings in Integrated Imaging at Purdue University Attached is an advertisement for faculty positions in the area of "Integrated Imaging" at Purdue. We are looking to find someone in the near term, and then to make multiple hires over the next two years. Tom ---------- Forwarded message ---------- From: Charles Bouman <bouman(a)purdue.edu> Date: Thu, May 3, 2012 at 8:32 AM Subject: Faculty openings in Integrated Imaging Hi all, Just to let you know, we have officially opened a search for faculty in the "Integrated Imaging" area. See below. So please distribute this information to anyone you think might be interested. Thanks! Charlie Purdue University College of Engineering and College of Science Faculty Opening in Integrated Imaging Purdue University?s College of Engineering and College of Science have identified imaging as a major thrust for cross-disciplinary research and education and are accepting applications for tenured and tenure track faculty (Assistant and Associate Professor) in this area. Imaging research has become the key to progress in fields such as medicine, biology, chemistry, physics, earth and atmospheric science; and the resulting technologies are addressing major human needs in healthcare, medicine, security, manufacturing, and communication. Purdue University has embarked on a new ?integrated-imaging? initiative to exploit the synergy between science and engineering, algorithms and devices, sensors and applications. This initiative will build on strengths and leverage the imaging capabilities of both Purdue Colleges and Purdue?s Discovery and Research Parks. Candidates must hold a Ph.D. degree in Engineering, Science or a related field. They should have a distinguished academic record, exceptional potential for world-class research, and a commitment to teach in both undergraduate and graduate programs. Specific research fields of interest in the integrated-imaging cluster include, but are not limited to electron and light microscopy, whole body imaging, image processing, inverse methods, multimodal imaging, hyperspectral imaging, and sensor systems. The successful candidate will teach undergraduate and graduate courses in topics related to integrated imaging, conduct research in their field of expertise, publish and present research findings, participate in professional activities, and advise graduate student research. The primary faculty appointment will be in a school of the College of Engineering or a department of the College of Science, and will depend on the candidate?s qualifications. Submit your application online at: https://engineering.purdue.edu/Engr/AboutUs/Employment/Applications. The application should include a cover letter, a complete and detailed vitae, and statements of research and teaching interests. Also, please include names, addresses, telephone numbers, and e-mail addresses for three or more references. For questions regarding the application process, please contact Marion Ragland (ragland(a)purdue.edu) Screening of applications will begin May 3, 2012 and will continue until the position is filled. A background check will be required for employment in this position. Purdue University is an Equal Opportunity/Equal Access/Affirmative Action Employer fully committed to achieving a diverse work force. _______________________________________________

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Rejoindre mon réseau sur LinkedIn
by Luisa Leo via LinkedIn 03 May '12

03 May '12

LinkedIn ------------ Luisa Leo souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Luisa Leo http://www.linkedin.com/e/-qq80um-h1s4irr1-14/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir l'invitation de Luisa Leo http://www.linkedin.com/e/-qq80um-h1s4irr1-14/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… ------------------------------------------ Quel est l'intérêt de faire partie du réseau de Luisa Leo ? Le réseau de Luisa Leo développera votre propre réseau : Si vous acceptez l'invitation de Luisa Leo, vous pourrez voir qui vous connaissez dans son réseau et demander à Luisa Leo de vous présenter. Appartenir à un réseau est toujours un plus pour votre carrière. -- (c) 2012, LinkedIn Corporation

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Freesurfer May 2012