Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

tksurfer crashes without error message
by Michelle Umali 20 Mar '12

20 Mar '12

Hi Freesurfers, I've been using Freesurfer for a while, and have had no trouble with launching tksurfer. But recently I have tried to view an inflated hemisphere of a subject I have had no problem viewing before. The window no longer opens. This the case for all of my subjects, with whom I have had no previous problems. Any suggestions would be most welcome. Thanks very much. Michelle Below is the terminal output. After this it just returns to the prompt without any error message.. /usr/local/freesurfer/subjects> tksurfer ld07 lh inflated subject is ld07 hemi is lh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects checking for nofix files in 'inflated' Reading image info (/usr/local/freesurfer/subjects/ld07) Reading /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: vertices=160638, faces=321272 surfer: double buffered window surfer: tkoInitWindow(ld07)

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freesurfer installation (fail)
by Daniël Höhle 20 Mar '12

20 Mar '12

Hello there, I''ve tried a couple installations of FreeSurfer as listed on the website. Though there seems to be a problem. Both linux tarballs seem to be designed for centos4, though that version is not supported anymore, so downloading is a pain, and accessing packages is out of the question. The same thing I encountered for Xubuntu 9.04. Freesurfer works, though, but it is (vritually) impossible to get information from a winfows network, because nfs-common needs to be installed, and since Xubuntu 9.04 is not supported anymore (a bit over a year now), I cannot install the packages needed to access data. Now I've downloaded Centos6 x86_32, I untarred the tarball, and I've set the environmental variables are listed. Though if I try the command "tkmedit bert orig.mgz" I get "/usr/local/freesurfer/tktools/tkmedit.bin: Command not found". I don't know whether I should try and tweak the Centos6 version, or whether freesurfer will not run on this OS all together. I got the impression that this project is still alive. Therefore I'd like to ask two questions: 1- can you, please, update the download section? FI virtual machine with Ubuntu 10.04, and tarballs and information for Centos6? 2- can you help me with installing this on Centos6? Kind regards, Daniël Höhle Scientific Programmer, Alan Turing Institute Almere, The Netherlands

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volume mapping
by Johnson 19 Mar '12

19 Mar '12

Hi This is Johnson, I am researcher at univ. of IL at chicago, I have a question regarding freesurfer: What is the transformation matrix that relates the freesurfer aparc+aseg space to the aparc+aseg-in-rawavg space, I am asking this question for the following reason: I have white matter fiber tracts in Diffusion space, I managed to transform it to aparc+aseg-in-rawavg space by registering the B0 to the brainmask-in-rawavg volume. Now I want to transform it to aparc+aseg space. thanks -- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical& Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email: jgadel2(a)uic.edu

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FS 5.1: white matter holes in wm.mgz
by Adam Martersteck 19 Mar '12

19 Mar '12

Hey all, Problem: I am getting white matter ‘holes’ of varying sizes on the wm.mgz I’ve uploaded 6 images to show an example of such a hole that was created. It is the same wm hole from all 3 views shown in brainmask.mgz and wm.mgz. The album with all 6 images can be found at photobucket.com/FS51 Background: The hole appears within the first or second recon-all (after edits made) They are appearing in multiple subjects If they do appear in a subject - it is usually between 2-3 per volume I am using FS 5.1 on a mac (recon on a linux) I am performing pial/wm/cp edits I was curious if anyone had ever run into this error and a solution for avoiding it in the future. Thanks in advance for the help! Adam Martersteck Cognitive Neurology and Alzheimer’s Disease Center brain.northwestern.edu

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bbregister
by Christopher Bell 19 Mar '12

19 Mar '12

I have run a bunch of cases through bbregister and overall it worked great! 315 out of about 325 cases the alignments were very good, but on 10 subjects it did very poorly. I can not so far find anything unusual about this data. Per earlier posts, I have tried the different initilization options with no luck. I also tried an fsl_rigid_register 6 DOF to create a starting .dat ,but that was way off too, maybe because it uses similar initilization information? I also saw the post to use --init-reg-out to save the init transform but I am not sure what to make of the output. This is aligning data that has been through the 1000FC pre-processing. This converts our RAS scans to RPI, and also de-obliques using AFNI. Would you suspect either of these steps as confusing bbregister? We are using dcm2nii (mricron) for dicom to nifti conversion.

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FreeSurfer Course in Amsterdam!
by Allison Stevens Player 19 Mar '12

19 Mar '12

Hi everyone, The Department of Radiology at VU University Medical Center in Amsterdam, Netherlands is hosting a FreeSurfer Course on June 27th through June 29th. Registration is now open. You can find details about course as well as the registration form on the following website: http://www.freesurfercourseamsterdam.nl/ Questions about the Amsterdam course should go to Veronica Popescu (info(a)freesurfercourseamsterdam.nl) Hope to see you there, Allison

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TRACULA: isn't the posterior distribution a probability?
by Juke Cha 18 Mar '12

18 Mar '12

Dear Dr. Yendiki and TRACULA experts, I was wondering what the unit of posterior distributions of reconstructed paths? By looking at the intensities, it ranges from 0 to ~150. I thought this is supposed to be a probability, but it's not? If it's in arbitrary unit, should I z-score them in order to show PD maps across subjects? Thanks for your help in advance. -- Juke Cha, M.S. Ph.D Candidate, Program in Neuroscience Laboratory for Computational Neurodiagnostics (LCN)<http://www.lcneuro.org/> Dept of Biomedical Engineering Stony Brook University School of Medicine email: cha(a)lcneuro.org office: 631-632-1992 fax: 631-632-3222

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Version differences of freesurfer for cortical thickness analysis
by Martin Lan 16 Mar '12

16 Mar '12

Hello, I am planning to do an analysis of cortical thickness, comparing a group of brain samples from patients to those of healthy control subjects. The laboratory that I am working in has freesurfer 4.5.0 loaded on our hardware. With our system, it would be labor intensive to load an updated version of freesurfer. My question is whether there would be significant disadvantages to using the 4.5.0 version for this function over the 5.1.0. Particularly, should we anticipate criticisms of reviewers of future manuscripts because of the use of the older version? Thank you in advance for your help, Martin

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LGI cluster correction
by Robustelli, Briana (NIH/NIMH) [F] 16 Mar '12

16 Mar '12

Dear Freesurfer Team, My group has been working with an lGI dataset for a while now and we were able to successfully complete a Monte Carlo cluster correction in FreeSurfer 4.5. It took a very long time but we did not receive any error messages. Now when we try to perform cluster corrections in 5.1, we receive this message, (Error: fwhm out-of-range (<1 or >30)!). So we wanted to check that the results we received from the cluster correction run in 4.5 are sound and to see if there is any solution to the 5.1 error. Thanks! Briana Robustelli -- Briana Robustelli Post-Baccalaureate IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C103 10 Center Dr MSC 1366 Bethesda, MD 20892 Phone: (301) 435-4491 Briana.Robustelli(a)nih.gov

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glut fatal error in tkmedit.bin visual with necessary capabilities not found
by Alex Liu 16 Mar '12

16 Mar '12

Hello all, I'm relatively new to freesurfer so this may be a simple fix. I was using freesurfer the other day and I came across the following message: GLUT: fatal error in tkmedit.bin visual with necessary capabilities not found. I'm using a mac laptop and I'm not sure if this is just an issue with computer settings. Any info on this matter would be greatly appreciated. Thank you. -- Alex

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