Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

.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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Re: [Freesurfer] 5.1.0 volume analysis in native space
by Douglas N Greve 03 May '12

03 May '12

If you just run selxavg3-sess, it will do the processing. If you want to run preproc-sess separately, then you can specify -per-session instead of -per-run to get things in native space. doug On 05/02/2012 02:55 PM, Maya Rosen wrote: > > Hi Doug, > Ok I see the -native flag in mkanalysis. But there is no -native flag > in preproc-sess. How do I go about preprocessing and analyzing the > data all in native volume space? > Thanks for your help, > Maya > > On Apr 26, 2012 4:39 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > There is (or should be) a -native flag to mkanalysis-sess > doug > > On 04/26/2012 11:09 AM, Maya Rosen wrote: > > Hi all, > > In v5.1.0 is there a way to do a volume analysis in native > space? I know when you do mkanalysis for the surface you can > use -surface self. But for the volume analysis the only flag I > see is -mni305. Is there some way to give it a native space > flag for the volume? > > Thanks! > > > Maya > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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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mri_convert error
by Kambiz Tavabi 03 May '12

03 May '12

Hello, The command mri_convert -it dicom -ot mgz 0001_9746dc8ab0544b3c8460cc2925682ba3.dcm 001.mgz gives the following output: mri_convert -it dicom -ot mgz 0001_9746dc8ab0544b3c8460cc2925682ba3.dcm 001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from 0001_9746dc8ab0544b3c8460cc2925682ba3.dcm... Starting DICOMRead2() dcmfile = /home/kambiz/data/freesurfer/ilabs/tmp/206/DICOM/0001_9746dc8ab0544b3c8460cc2925682ba3.dcm dcmdir = /home/kambiz/data/freesurfer/ilabs/tmp/206/DICOM Ref Series No = 301 Found 707 files, checking for dicoms WARNING: tag image orientation not found Found 705 dicom files in series. WARNING: tag image orientation not found First Sorting Computing Slice Direction Vs: 85.2923 -138.9 161.601 Vs: 0.371599 -0.605155 0.704061 Second Sorting Counting frames nframes = 1 nslices = 705 ndcmfiles = 705 MRIalloc(0, 0, 705): bad parm ERROR: mri alloc failed I am running freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on RedHat 5.8 I don't understand what the problem is? Thanks in advance Kambiz -- ------------------------------------------------------------ Kambiz Tavabi PhD Institute for Learning & Brain Sciences 1715 Columbia Road N Portage Bay Building Box 357988 University of Washington Seattle, WA 98195-7988 Tel: 206-221-6415 ------------------------------------------------------------

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Freeview chrash
by Focke, Niels 03 May '12

03 May '12

Dear experts, I have experienced some problems with freeview. When loading a surface (both for my locally generated surfaces as well as for "bert" surfaces) the program exits (progress bar at approx. 10%) with this message: MatrixMultiply: m2 is null! The problem happens both for command line loading and GUI loading. Volume loading/viewing works fine. Has anyone had a similar problem? Or (even better) has a fix available? Version information: FREESURFER_HOME: /tools/freesurfer/live Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: CentOS release 5.7 (Final) Kernel info: Linux 2.6.18-274.el5 x86_64 Many thanks, Niels __________________________________________________________________________ Dr. Niels Focke Klinische Neurophysiologie UMG - Universitätsmedizin Göttingen

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reg-feat2anat error in Ubuntu 12.04 and a workaround
by Auer, Tibor 03 May '12

03 May '12

I have recently upgraded my Ubuntu system from 11.10 to 12.04. Before the upgrade I had no problem at all! After the upgrade the "reg-feat2anat" stopped working: it gave an error when converting the subject/mri/brainmask.mgz to featdir.feat/reg/freesurfer/tmp/refvol.fslregister.nii. However, when I do the conversion manually before the "reg-feat2anat", it works without further error. Is there any explanation for this behavior? Auer, Tibor M.D. Ph.D. Biomedizinische NMR Forschungs GmbH am Max-Planck Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Germany Phone/Work: +49-(0)551-201-1725 Phone/Home: +49-(0)551-387-0076 Mobile: +49-(0)176-8012-7921 Mail: tauer(a)mpibpc.mpg.de

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