Freesurfer June 2013

freesurfer@nmr.mgh.harvard.edu

170 participants
298 discussions

How does freesurfer take the individual landmarks of different regions take into acccount
by Klein, Holger 11 Jun '13

11 Jun '13

Dear Bruce et al., Submitting a paper in which I use freesurfer for the analysis of the auditory cortex, I was asked how freesurfer actually takes individual boundaries (e.g. of Heschl's gyrus) into account? Both atlases (Desikan and Destrieux) are based on about 10-20 subjects. How are these boundaries transferred to other subjects? As far as I understood the description of freesurfer there aren't any templates (or some kind of masks) which are put on the subjects to analyse. What's the "secret" or principle behind the individual analysis to receive reliable data for every ROI of every subject (in a nutshell)? Thanks in advance, best wishes, Holger

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How to measure the surface dimension in a mask image after mri_glmfit?
by Glen Lee 11 Jun '13

11 Jun '13

Dear freesurfer users I'm wondering if there is any way of figuring out the surface size within a mask image (mask.mgh) which is generated after running a group-level GLM analysis (2nd RFX) using mri_glmfit. As I'm thinking, this may be: number of vertex by dimension of one vertex (1mm). But I could be wrong and let me know if anyone knows the solution. -Glen fyi) the group analysis was performed in freesurfer sym space.

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Cross-sectional v5.1 vs. Longitudinal v4.4
by MCLAREN, Donald 11 Jun '13

11 Jun '13

Dear All, If I had to choose between longitudinal processing v4.4 or cross-sectional processing v5.1 for analyzing longitudinal data, what processing stream should I choose? Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

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Re: [Freesurfer] environment variable FREESURFER_HOME
by zkaufman＠nmr.mgh.harvard.edu 11 Jun '13

11 Jun '13

Pablo, The .cshrc and .bashrc files we are referring to are not Freesurfer files and do not come with the Freesurfer distribution. They are files that can (although not always) exist in the home directory of your computer. Do not modify the the .csh or .sh files that come with Freesurfer. That is for the expert user. If you want to use Freesurfer just open a command line and type the following: (if using csh) setenv FREESURFER_HOME Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh (if using bash) export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh If you dont want to type these commands everytime you want to start using freesurfer than you can add these lines to your .csh and .bashrc *in your home directory*. If those files do not exist than you may create them *in your home directory* and simply add those two lines to the file. -Zeke > Dear Freesurfer experts, > I am trying to install free surfer. > It seems that my downloaded version does not have a .cshrc file. I only > have an .sh and .csh file. > All the edits (i.e.,setenv FREESURFER_HOME Applications/freesurfer/ source > Applications/freesurfer/SetUpFreeSurfer.csh) that I tried to the .csh file > give me "command not found". > > Any suggestion would be highly appreciated. > Pablo > > Thank you for your response. > It seems that my downloaded version does not have a .cshrc file. I only > have an .sh and a .csh. > What would you recommend to do? Should I reinstall FreeSurfer? > Thanks. > Pablo > >> Date: Fri, 7 Jun 2013 18:16:56 -0400 >> From: zkaufman(a)nmr.mgh.harvard.edu >> To: pablonajt(a)hotmail.com >> Subject: Re: [Freesurfer] environment variable FREESURFER_HOME >> >> There should be a file called ".cshrc" in your home directory. Add the >> two lines to that file. >> >> -Zeke >> >> On 06/07/2013 05:53 PM, pablo najt wrote: >> > Can anyone advice me on how to set the environment variable >> > FREESURFER_HOME for installing it in OS X 10.6.8 (with XQuartz >> installed)? >> > >> > My directory for Freesurfer:*/Applications/freesurfer* >> > * >> > * >> > I know I also have to add: >> > >> > setenv FREESURFER_HOME /Applications/freesurfer >> > >> > source $FREESURFER_HOME/SetUpFreeSurfer.csh >> > But I am not sure where exactly I should add these lines. >> > >> > Do I need to edit the .csh file in Freesurfer. >> > >> > How should I do this? using Text Edit from apple would work? >> > Thanks, >> > Pablo >> > >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> >> >> 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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Mean Regional Thickness
by MCLAREN, Donald 11 Jun '13

11 Jun '13

Has anyone published the mean cortical thickness of healthy older adults for all the Freesurfer ROI? I've only been able to find papers that report a of subset of the ROIs. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

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Fwd: Talairach Positioning in Horizontal View
by Peter Boulos 11 Jun '13

11 Jun '13

I am very new to the software and have just begun assessing Talairach outputs for my subjects. I am confused in that I cannot seem to find a balance I am happy with between positioning of the green lines in both the horizontal and sagittal views for multiple subjects. I opened the talairach output with the following command (tkregister2 --mgz --s SUBJID --fstal --surf orig) and everything looked perfectly aligned for all the subjects I have tried in both the coronal and sagittal views but in the horizontal view the green lines went well off the back of the brain. I have attached a screenshot. I tried to translate the brain but that did not seem to solve my issue and I realized I needed to scale the length of the brain. When I did that I was more pleased with the outcome but the corpus callosum did not match up nearly as well after I did that (second attached screenshot) and that was the primary landmark I was using to pass my images in terms of talairach output assessment. Do you have any advice for me? Peter

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Re: [Freesurfer] Problem after installation of the newest security updates for MacOSX
by Jürgen Hänggi 11 Jun '13

11 Jun '13

Hi Zeke As suggested, I deleted the /opt/X11 directory and reinstalled Xquartz and everything works fine again. Thanks a lot Cheers Jürgen On [DATE], "Z K" <[ADDRESS]> wrote: > Jurgen, this is odd. I have never seen an error from X11/XQuartz on Macs > complaining about version numbers... > > Are you saying everything worked fine before the security updates? And > then immediately afterward the updates tkmedit stopped working? If so, > my suggestion would be to delete the /opt/X11 directory and reinstall > XQuartz from this link: > > http://xquartz.macosforge.org/landing/ > > -Zeke > > On 06/11/2013 12:56 PM, Jürgen Hänggi wrote: >> Hi Zeke >> >> Here ls -l in /usr/ >> >> lrwxr-xr-x 1 root wheel 8 Mar 27 10:54 X11 -> /opt/X11 >> lrwxr-xr-x 1 root wheel 8 Mar 27 10:54 X11R6 -> /opt/X11 >> drwxr-xr-x 1091 root wheel 37094 Jun 11 10:59 bin >> drwxr-xr-x 4 root wheel 136 Oct 24 2010 etc >> drwxr-xr-x 271 root wheel 9214 Apr 26 2012 include >> drwxr-xr-x 387 root wheel 13158 Jun 11 10:59 lib >> drwxr-xr-x 111 root wheel 3774 Jun 11 10:59 libexec >> drwxrwxr-x 7 root admin 238 Dec 15 2010 llvm-gcc-4.2 >> drwxr-xr-x 10 root wheel 340 Jan 22 10:28 local >> drwxr-xr-x 237 root wheel 8058 Jun 11 10:59 sbin >> drwxr-xr-x 74 root wheel 2516 Apr 24 09:17 share >> drwxr-xr-x 4 root wheel 136 Dec 14 2009 standalone >> >> >> ls -l in /opt/ >> >> total 0 >> drwxr-xr-x 8 root wheel 272 Sep 28 2012 X11 >> >> Thanks in advance >> Regards >> Jürgen >> >> On [DATE], "Z K" <[ADDRESS]> wrote: >> >>> Hello Jurge, >>> >>> Can you please type "ls -l" in the /usr directory and "ls -l" in the >>> /opt directory and email me the output? >>> >>> -Zeke >>> >>> On 06/11/2013 08:51 AM, Jürgen Hänggi wrote: >>>> Dear FS experts >>>> >>>> After the installation of the newest Mac OS X security updates, the >>>> following error occurred: >>>> >>>> [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] >>>> juergenhaenggi% >>>> tksurfer bert lh pial >>>> dyld: Library not loaded: /opt/X11/lib/libX11.6.dylib >>>> Referenced from: /usr/X11/lib/libGL.1.dylib >>>> Reason: Incompatible library version: libGL.1.dylib requires version >>>> 10.0.0 or later, but libX11.6.dylib provides version 9.0.0 >>>> Trace/BPT trap >>>> [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] >>>> juergenhaenggi% >>>> >>>> >>>> Any idea to fix it easily is highly appreciated. >>>> >>>> Cheers >>>> Jürgen Hänggi >>>> >>>> --------------------------------------------------------------------------->>>> - >>>> Jürgen Hänggi, Ph.D. >>>> Division Neuropsychology >>>> Institute of Psychology >>>> University of Zurich >>>> Binzmuehlestrasse 14, PO Box 25 >>>> 8050 Zurich, Switzerland >>>> 0041 44 635 73 97 (phone office) >>>> 0041 76 445 86 84 (phone mobile) >>>> 0041 44 635 74 09 (fax office) >>>> BIN 4.D.04 (office room number) >>>> j.haenggi[at]psychologie.uzh.ch (email) >>>> http://www.psychologie.uzh.ch/neuropsy/ (website) >>>> http://www.juergenhaenggi.ch (private website) >>>> >>>> This e-mail (and any attachment/s) contains confidential and/or privileged >>>> information. If you are not the intended recipient (or have received this >>>> e-mail in error) please notify the sender immediately and destroy this >>>> e-mail. Any unauthorised copying, disclosure or distribution of the >>>> material in this e-mail is strictly forbidden. >>>> --------------------------------------------------------------------------->>>> - >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> >>> >>> 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. >>> >> >> >> ---------------------------------------------------------------------------- >> Jürgen Hänggi, Ph.D. >> Division Neuropsychology >> Institute of Psychology >> University of Zurich >> Binzmuehlestrasse 14, PO Box 25 >> 8050 Zurich, Switzerland >> 0041 44 635 73 97 (phone office) >> 0041 76 445 86 84 (phone mobile) >> 0041 44 635 74 09 (fax office) >> BIN 4.D.04 (office room number) >> j.haenggi[at]psychologie.uzh.ch (email) >> http://www.psychologie.uzh.ch/neuropsy/ (website) >> http://www.juergenhaenggi.ch (private website) >> >> This e-mail (and any attachment/s) contains confidential and/or privileged >> information. If you are not the intended recipient (or have received this >> e-mail in error) please notify the sender immediately and destroy this >> e-mail. Any unauthorised copying, disclosure or distribution of the >> material in this e-mail is strictly forbidden. >> ---------------------------------------------------------------------------- >> >> >> >> >> ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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importing my data
by clelia pellicano 11 Jun '13

11 Jun '13

Dear all, I'm trying to import my data in Freesurfer. I have it on a folder on my desktop. I set my SUBJECTS_DIR variable to my subjects directory (other folder on my desktop). When I run recon-all -i paths_to_myimputfiles -subjid my_sub_name, I got: [cpellica@wmen-ps2208 freesurfer]$ recon-all -i /home/cpellica/Desktop/MRIs%201-5/001/IM-0003-0001.dcm -subjid 001 ERROR: cannot find /home/cpellica/Desktop/MRIs%201-5/001/IM-0003-0001.dcm Linux wmen-ps2208 2.6.32-358.11.1.el6.x86_64 #1 SMP Wed May 15 10:48:38 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Tue Jun 11 17:24:51 BST 2013 I don't understand why it is not finding my data since they are on my desktop. Could you help me? Thanks C.

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Re: [Freesurfer] tkmedit on ssh remote machine error
by Jon Wieser 11 Jun '13

11 Jun '13

hi Zeke, were you able to find a solution to my problem with running tkmedit on a remote machine? thanks Jon ----- Original Message ----- From: "Z K" <zkaufman(a)nmr.mgh.harvard.edu> To: "Jon Wieser" <wieser(a)uwm.edu> Sent: Thursday, May 30, 2013 1:42:41 PM Subject: Re: [Freesurfer] tkmedit on ssh remote machine error Hmm that is a very strange error you are encountering. Im trying to duplicate the issue on my end. I only have one Mac 10.6 and one Mac 10.7 machine but Ill let you know what I find and hopefully I can come up with a solution. -Zeke On 05/30/2013 02:37 PM, Jon Wieser wrote: > both machines have Mac OS X 10.6.8 > > the tkmedit works fine when not logged in remotely > there is no error and the brain image is there > Jon > > ----- Original Message ----- > From: "Z K" <zkaufman(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Thursday, May 30, 2013 12:16:55 PM > Subject: Re: [Freesurfer] tkmedit on ssh remote machine error > > Jon, > > I have not seen or heard of this error before... are both machines Mac > OSX 10.6.8? Also, will the same command will produce a brain image when > not logged in remotely? > > -Zeke > > On 05/30/2013 12:43 PM, Jon Wieser wrote: >> >> hi freesurfer folks >> >> I'm ssh'ing to from one MAc to another >> X11 is on both machines >> MAC OS X 10.6.8 >> >> When I start TKmedit with: (freesurfer files are in the freesurfer directory) >> >> tkmedit freesurfer brainmask.mgz -aux T1.mgz >> >> >> I get the errors: >> Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: kCGErrorIllegalArgument: _CGSFindSharedWindow: WID 349 >> Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. >> Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: kCGErrorIllegalArgument: CGSSetWindowSendExposed: Invalid window 0x15d >> Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: unknown error code: invalid drawable >> error: xp_attach_gl_context returned: 2 >> >> >> >> tkmedit GUI opens and the image window opens, but the image window is blank (white) , (no image of the brain) >> >> >> >> >> i have set X11forwarding to yes in the /etc/sshd_config file >> so xeyes works ok remotely >> Jon >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > > -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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License problem
by Claus Svarer 11 Jun '13

11 Jun '13

Hi We have just updated one of our Linux servers from OpenSuse v. 12.1 to 12.3. After the update we get the following license error message for some of the freesurfer commands: csvarer@hevesy:/usr/local/nru/freesurfer> tkmedit -help -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /usr/local/nru/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- W have another server still running the older OpenSuse version and there it works without any problems. There hasn't been done any changes to the freesurfer installation directory and it is the same shared NFS mounted directory at both servers. Please help us finding out how to correct this problem so we can use Freesurfer again. Thanks for the help Claus Svarer

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Freesurfer June 2013