Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

problem with skullstrip- shoulders and neck remaining
by Julia Hill 09 Nov '11

09 Nov '11

Hi there, I am having difficulties with one of my images. On first inspection, freesurfer had performed a bad skull strip, leaving the base of the skull plus what looked to be the shoulders and neck. I decreased the watershed to 5, and the shoulders/neck still appeared, so i decreased to 2 and now sections of the brain have disappeared (see attached), do you know how i can fix this? Many thanks , Julia Hill Research Assistant School of Psychiatry University of New South Wales Previously Prince of Wales Medical Research Institute www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia T +61 2 9399 1268

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Resize window using Tcl command
by Jeff Sadino 09 Nov '11

09 Nov '11

Hello, I was wondering if there is a Tcl command to resize the window. I saw this thread, but it would not work on my computer, and I don't see any documentation in the tkmedit tcl scripting guide. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02600.html Thank you, Jeff Sadino

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Fwhm from mgh file produced by mri_glmfit
by Knut J Bjuland 09 Nov '11

09 Nov '11

Hi Is there any way to get fwhm information from an mgh produced by mri_glmfit? I have only the mgh file produce by mri_glmfit. Knut J

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End-of-line detection in text file
by Ed Gronenschild 09 Nov '11

09 Nov '11

Hi, After editing a text file holding the b vecs to be supplied as input to dt_recon this tool did not interpret the text file correctly. It turned out that dt_recon did not recognise the end-of line character in this file: this was decimal code 13 (called "CR"). It seems that dt_recon only accepts decimal code 10 (called "LF"). Is it possible to change dt_recon? I'm on a Mac, OSX 10.6.8. Cheers, Ed

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Compilation warnings as errors
by Panagiotis Foteinos 08 Nov '11

08 Nov '11

Hello list. I am compiling the source code and I get some warnings as errors. Is there a good reason that the switch -Werror is activated, or I can safely deactivate it? Could I assume that the warnings I get are harmless? Best Regards, Panagiotis Foteinos

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selxavg3 out of memory
by Po-Jang (Brown) Hsieh 08 Nov '11

08 Nov '11

Dear Doug, I saw your reply to this question a while ago. I'm using a mac pro with 16G memory but having the same problem. Do you know if this is a matlab memory issue (matlab R2009a) or an overall memory issue of the machine? I'd appreciate if you can give me some helps. (I have 12 runs, each run has 200 TRs and 20 events, TR=2s) Thanks very much! Brown ps. Here are the commands and error messages: mkanalysis-sess -analysis $ANALYSIS -TR 2 -paradigm $PARAFILE -event-related -funcstem $FUNCSTEM -nconditions 9 -mcextreg -runlistfile $RLF -fsd bold -fir 10 30 -native selxavg3-sess -s $SUBJECTID -df sessdir -analysis $ANALYSIS -no-con-ok >>>> Whitening Computing whitening matrices MATLAB(19078,0xb0987000) malloc: *** mmap(size=1382400000) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug ??? Out of memory. Type HELP MEMORY for your options. Error in ==> fast_selxavg3 at 603 Sinv = zeros(ntptot,ntptot,flac0.acfbins); >> pure virtual method calledOpening log file: /var/root/java.log.19078 Abort ------------------------------------------ ERROR: fast_selxavg3() failed\n >>>> I think you might need a bigger computer. A run of that data set will require almost 1G, and there are places in the code where several data structures of the same size will need to exist simultaneously, so you can easily use 2 or 3 or 4 G to process a single run. In theory you could divide them up into smaller bits as long as you handle the stimulus schedule files properly. doug Schadwinkel, Stefan wrote: >*Hi,*>**>*as I tried to show in the posting, I tried it on 3 Machines:*>**>*1) Linux, 1 GB memory: out of memory during OLS Residual Pass, then Java crashes*>*2) Linux, 2 GB memory: out of memory during Whitening*>*3) Mac (Mac OS X 10.5), 4 GB memory: as well: out of memory during Whitening*>**>*Thanks a lot & best regards,*>**>*Stefan Schadwinkel * -- Po-Jang (Brown) Hsieh Neuroscience and Behavioral Disorders Program Duke-NUS Graduate Medical School 8 College Road, Singapore 169857 -- Lab website: Brain & Consciousness Lab<https://sites.google.com/site/brainconsciousnesslab/> <http://brownhsieh.blogspot.com/>

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Re: [Freesurfer] Visualization of FreeSurfer-defined ROI
by Simmons, Andy 08 Nov '11

08 Nov '11

Dear Doug, What would the equivalent process for a surface rather than a volume ? Best wishes, Andy SImmons Date: Fri, 04 Nov 2011 17:30:47 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Visulaization of FreeSurfer-defined ROI To: Jade <jadeinny8(a)gmail.com<mailto:jadeinny8@gmail.com>> Cc: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <4EB45987.2040001(a)nmr.mgh.harvard.edu<mailto:4EB45987.2040001@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Try running mri_binarize with the --match option. The match value should be the id number for your ROI as defined in $FREESURFER_HOME/FreeSurferColorLUT.txt (eg, left hippo is 17). You can then load this as a segmentation or as an overlay in tkmedit. doug Jade wrote: > Hello Freesurfer experts, > > I am a beginner in using Freesurfer. > > I want to make a figure illustrates a specific area of ROIs (e.g., > lh. hippocampus). How can I visulaize the Freesurfer definded ROIs? > > Thanks in advance! ---- Dr Andy Simmons Reader in Neuroimaging & Consultant Clinical Scientist Centre for Neuroimaging Sciences and NIHR Biomedical Research Centre Institute of Psychiatry, Box P089 Kings College London De Crespigny Park London, SE5 8AF, UK Email - andy.simmons(a)kcl.ac.uk Webpage - http://www.iop.kcl.ac.uk/staff/profile/default.aspx?go=10338 Directions - http://www.iop.kcl.ac.uk/virtual/?path=/about/how-to-find-the-institute-of-… ResearcherID - http://www.researcherid.com/rid/B-8848-2008 Fax +44 (0)203 228 2116 [cid:image001.png@01CC9E47.37F065F0]<http://msc-neuroimaging.com/>

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Upgraded Freesurfer: old version no longer working + recon-all error in 5.1
by Jennifer Addicks 08 Nov '11

08 Nov '11

Hello, I have been successfully running FreeSurfer 4.5 on my MacOSX 10.5.8 with no issues. I recently installed FreeSurfer 5.1 to a separate directory on the same laptop to analyze a new dataset and I am now having various issues with both FreeSurfer versions. 1. For Version 4.5, I path the freesurfer directories as follows (identical to before installing new program): setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir source $FREESURFER_HOME/SetUpFreeSurfer.csh --------- freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir MNI_DIR /Applications/freesurfer/mni The issue is that now various commands are no longer found in version 4.5. For example when typing tkmedit, tksurfer or qdec, I get the following type of error: tkmedit.bin: Command not found. Is it possible that, although I installed version 5.1 in a separate directory, that some files were deleted or moved in version 4.5? Is my 4.5 license no longer valid now that I have installed version 5.1 with a new license? It is confusing since some commands appear to function, such as mri_convert and recon-all, but anything involving a GUI seems not to function. 2. For version 5.1, I believe the program is successfully installed and pathed. I have been able to use it to convert files to mgz, tkmedit and tksurfer work fine, however, I get the same error each time I run recon-all with each participant (one of which was previously successfully processed using version 4.5). The recon-all error occurs early during motion correction of the 2 structural runs: Resolution: 0 S( 512 512 352 ) T( 512 512 352 ) Iteration(f): 1 (subsample 200) mri_robust_template(3271) malloc: *** mmap(size=1048576) failed (error code=12)*** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(512, 512, 352): could not allocate 1048576 bytes for 258th slice Cannot allocate memory Darwin jennifer-phillipss-macbook-pro.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 recon-all -s SS002 exited with ERRORS at Fri Nov 4 10:04:46 EDT 2011 Any ideas on what might be causing this error? I have 4 GB memory. thanks, Jennifer Addicks University of Ottawa

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Fwd: A question about recon-all
by nooshin n.zade 08 Nov '11

08 Nov '11

Dear Freesurfer Group I have found a problem in running my subjects. With "recon-all -autorecon1 -autorecon2 -autorecon3 -subjid N?" I ran several subjects after making corrections, but suddenly I received error message as following, and I can not run rest of the subjects. It is saying the subject is already running but I am running the subject elsewhere. Can you please help me to face this issue. Thanks a lot in advance. INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /Users/christine/CorrectedOnes Actual FREESURFER_HOME /Applications/freesurfer -rw-r--r-- 1 christine staff 469592 Nov 4 12:46 /Users/christine/CorrectedOnes/N3237c/scripts/recon-all.log Darwin administrators-mac-pro.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 ERROR: it appears that recon-all is already running for N3237c based on the presence of /Users/christine/CorrectedOnes/N3237c/scripts/IsRunning.lh+rh. It could also be that recon-all was running at one point but died in an unexpected way. If it is the case that there is a process running, you can kill it and start over or just let it run. If the process has died, you should type: rm /Users/christine/CorrectedOnes/N3237c/scripts/IsRunning.lh+rh and re-run. Or you can add -no-isrunning to the recon-all command-line. The contents of this file are: ---------------------------------------------------------- ------------------------------ SUBJECT N3237c HEMI lh rh DATE Wed Nov 2 12:03:39 EDT 2011 USER christine HOST administrators-mac-pro.local PROCESSID 40999 PROCESSOR i386 OS Darwin Darwin administrators-mac-pro.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 $Id: recon-all,v 1.313.2.6 2010/08/04 15:50:56 nicks Exp $ ---------------------------------------------------------- Best Regards --------------------------------------------------- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ** * * * * -- Best Regards --------------------------------------------------- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ** * * * *

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norm.mgz
by YUMI MAEDA 08 Nov '11

08 Nov '11

Hi, I had 2 bad blocks in freesurfer/subject/mri/norm.mgz on my disk drive. I had to delete mri/norm.mgz. Is there any way that I can just creat norm.mgz? or do I need to do recon-all? thank you. YUMI

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