Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30096 discussions

'Bus error' when running commands from the "Testing your FreeSurfer Installation" wiki page
by Swartz, Max 24 May '13

24 May '13

Happy Friday! I was able to install FreeSurfer v5.3.0 on my personal Macbook (2.4 GHz Intel Core i5 processor, 4 GB 1067 MHz DDR3, Mac OS X 10.6.8). Unfortunately, I'm still getting some error messages as I run through the commands on the "Testing your FreeSurfer Installation" page in the manual. Originally, I was receiving the following error message when trying to run the "tkmedit" commands (such as "tkmedit bert norm.mgz"): - "dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib" - Followed by "Referenced from: /Applications/freesurfer/tktools/tkmedit.bin Reason: image not found" To remedy the situation, I downloaded and installed XQuartz. Now the error message I receive is simply "Bus error". It also appears when I try to run the "tksurfer" and "qdec" commands as well. I have not yet tried the "recon-all" command. If you have any ideas how I can fix this or any suggestions, I'd really appreciate it. Thanks, and have a great weekend, Max

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FreeSurfer v 5.3.0 compatibility with Mac OS X 10.4.11
by Swartz, Max 24 May '13

24 May '13

Hello, I am working as a research assistant for the summer with the University of Cincinnati's Psychiatry department in the Division of Bipolar Disorders Research under Cal Adler and Melissa DelBello. We are looking to start utilizing FreeSurfer; however, I am getting some error messages when trying to perform most of the tasks on the "Testing your FreeSurfer installation" page in the wiki ( https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer ). The most common of the error messages I am receiving is "Exec format error. Binary file not executable." The Mac I am trying to run FreeSurfer on has a dual 2 GHz PowerPC G5 processor and 4 GB DDR SDRAM, and is running Mac OS X 10.4.11 (Tiger). I have been trying to use FreeSurfer v5.3.0 for SnowLeopard OS X 10.6 (32b Intel). Should this version compatible with my computer? We are thinking that our error messages are the result of either operating system incompatibility or not having all of the necessary privileges on our account (which can be fixed through IT). Any insight you can provide regarding the compatibility of FreeSurfer v5.3.0 on Mac OS X 10.4 Tiger systems would be incredibly helpful. Thanks so much, Max Swartz

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Bug report: QDEC
by Tudor Popescu 24 May '13

24 May '13

Just reporting a GUI bug in QDEC: after setting a different FDR threshold and pressing the "Set Using FDR" button, more often than not the results image doesn’t change accordingly. I noticed that the button only has an effect after moving around the QDEC window and/or waiting a minute or so. Hope that helps, Tudor

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p-value visualization
by Ludovici, Katharine (NIH/NIMH) [F] 24 May '13

24 May '13

Hello, We are attempting to compare surface area for 46 regions of interest in subjects versus controls. We've created a list of p-values for each ROI using R Studio to compare the two groups. Is there any way to visualize these p-values mapped on to the ROI's? Thanks very much, Katie Ludovici Postbaccalaureate IRTA National Institute of Mental Health Child Psychiatry Branch 301-435-5557

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problem with alignment of labeling files generated from the rh.area file
by Tina Jeon 24 May '13

24 May '13

Hello Freesurfers, I have created labeling files from a subject using the area file (previously named base). The label file corresponds to the freesurfer generated cortical label, ctx-rh-bankssts, which I have attached in this email. The labeling files should be the same, however, there are some discrepancies in the files: 1). There is a slight offset in the vertices. 2). A reduced number of vertices in the .label file created from the area file. 3). The vertex numbers are numbered -1. Our goal is to overlay a custom atlas onto a cortical surface generated from amira in freesurfer. Can you please tell how to transform the labeling files so that I can successfully overlay them? I have attached all three files for you. rh.rh_label_2001.label is the labeling file created from the base file, rh.ctx-rh-bankssts.label is the label from freesurfer and the rh.base file I have sent to Bruce the file is too large. When I overlay the rh.rh_label_2001.label and other labels generated from the base file, only parts of the temporal lobe are overlayed. Thank you in advance, Tina Jeon UT Southwestern Medical Center '14 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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A question of running fsfast in mac
by Yongxia Zhou 24 May '13

24 May '13

Dear Freesurfer experts: hi, I'm one of the attendees of the multi-modality training program. I had tried running fsfast in the mac and got an error message. Below is the detail information. Any of your suggestions is highly appreciated and thank you very much. -Sharon OS: Mac OS X 10.5.6 [YongxiaZhous-MacBook:~/Desktop/DICOM/13051914] Young% pwd /Users/Young/Desktop/DICOM/13051914 [YongxiaZhous-MacBook:~/Desktop/DICOM/13051914] Young% selxavg3-sess -s sess01 -analysis /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/001/test01.sm05.lh -no-preproc -c music_silence.mat -------------------------------------------------------------- selxavg3-sess logfile is /Users/Young/Desktop/DICOM/13051914/log/selxavg3-sess-bold-test01.sm05.lh-130524090501.log -------------------------------------------------------------- ------------------------------------------- /Users/Young/Desktop/DICOM/13051914/sess01 Fri May 24 09:05:02 EDT 2013 anadir = /Users/Young/Desktop/DICOM/13051914/sess01/bold/test01.sm05.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2007 The MathWorks, Inc. Version 7.4.0.287 (R2007a) January 29, 2007 Warning: Duplicate directory name: /Users/Young/matlab. Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. > In hgrc at 132 In matlabrc at 105 Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. > In path at 110 In startup at 5 In matlabrc at 255 Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. > In path at 110 In startup at 14 In matlabrc at 255 >> >> >> >> >> >> >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# sess01 ############################### /Users/Young/Desktop/DICOM/13051914/sess01 ------------------------- $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m /Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m /Applications/freesurfer/matlab/MRIread.m ------------------------- outtop = /Users/Young/Desktop/DICOM/13051914 Extension format = nii.gz 1 music_silence.mat ??? Error using ==> MRIread at 76 ERROR: cannot determine format of /Users/Young/Desktop/DICOM/13051914/sess01/bold/001/fmc.siemens.sm5 (MRIread) Error in ==> flac_customize at 87 mri = MRIread(fstem,1); Error in ==> fast_selxavg3 at 65 flac0 = flac_customize(flac0); >> 2013-05-24 09:05:32.710 MATLAB[65661:60b] Process manager already initialized -- can't fully enable headless mode. ------------------------------------------ ERROR: fast_selxavg3() failed\n

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Re: [Freesurfer] command not found
by Louis Nicholas Vinke 24 May '13

24 May '13

Hi Clelia, What do you run to source FS and do you get any output in your terminal after doing so? What operating system are you running? You might try using c-shell instead of bash. -Louis On Fri, 24 May 2013, clelia pellicano wrote: > Hi Louis, > thank you for your answer. > I sourced freesurfer again, but I still get 'command not found'. > What can I try? > Thank you, > > Clelia > > > On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> wrote: > Hi Clelia, > If this is in a new terminal then you'll have to source freesurfer again. See here for details: > https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration > -Louis > > On Wed, 22 May 2013, clelia pellicano wrote: > > Hi, > I have run recon-all -s bert -all to try my installation and it worked. > Now, when I try to use other command (and also again recon-all -s bert -all) I always get this: > > dyn1097-8:subjects cpellica$ tkmedit bert orig.mgz > -bash: tkmedit: command not found > dyn1097-8:subjects cpellica$ tkmedit -s bert orig.mgz > -bash: tkmedit: command not found > dyn1097-8:subjects cpellica$ tksurfer -s bert rh pial > -bash: tksurfer: command not found > dyn1097-8:subjects cpellica$ qdec > -bash: qdec: command not found > dyn1097-8:subjects cpellica$ recon-all help > -bash: recon-all: command not found > dyn1097-8:subjects cpellica$ recon-all -s bert -all > -bash: recon-all: command not found > > > I don't know how to do. Please, could you help me? > > Thanks > > Clelia > > > > > 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. > > > >

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Rejoindre mon réseau sur LinkedIn
by Melina Papalampropoulou-Tsiridou 24 May '13

24 May '13

LinkedIn ------------ Melina Papalampropoulou-Tsiridou 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 Melina Papalampropoulou-Tsiridou http://www.linkedin.com/e/-qq80um-hh3d1hd2-1o/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir le profil de Melina Papalampropoulou-Tsiridou http://www.linkedin.com/e/-qq80um-hh3d1hd2-1o/rso/228073899/LikC/name/66471… ------------------------------------------ Vous recevez des invitations par e-mail. Cet e-mail est destiné à Freesurfer List. Découvrez pourquoi nous avons inclus ceci : http://www.linkedin.com/e/-qq80um-hh3d1hd2-1o/plh/http%3A%2F%2Fhelp%2Elinke… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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freesurfer 5.2 mac download link
by Jonathan Holt 23 May '13

23 May '13

can't seem to find it, would appreciate a link! jon

2 1

Problem with a subject using recon-all command
by stdp82＠virgilio.it 23 May '13

23 May '13

Hi list, I'm performing recon-all -all -notal-check -i $SUBJECTS_DIR/T1_STRUCT.nii.gz -subject SUBJECTS_DIR -cw256 on a T1 with following info:data_type INT16dim1 280dim2 240dim3 240dim4 1datatype 4pixdim1 0.5999908447pixdim2 1.0416666269pixdim3 1.0416666269pixdim4 0.0000000000cal_max 0.0000cal_min 0.0000file_type NIFTI-1+ and I have this error (2) Problem with the least square interpolation for CSF_MAX GLOBAL CSF_MIN=0, CSF_intensity=6, CSF_MAX=55 , nb = 36036 RIGHT_CER CSF_MIN=0, CSF_intensity=6, CSF_MAX=39 , nb = 3042 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=32 , nb = 3852 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=41, CSF_MAX=179 , nb = 14652 LEFT_BRAIN CSF_MIN=0, CSF_intensity=41, CSF_MAX=99 , nb = 14058 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=12 , nb = 432mri_watershed Error: GLOBAL region of the brain empty !Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s SUBJECTS_DIR exited with ERRORS at Fri May 24 00:04:27 CEST 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Complete .log file is also attached. What's happen? Thanks, Stefano

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