Freesurfer

freesurfer@nmr.mgh.harvard.edu

10 participants
30093 discussions

dual installation question
by Joshua Lee 22 Feb '13

22 Feb '13

If I want to install the new Freesurfer version but retain the older Freesurfer install as well, what issues might I face? Is it simply sourcing the usual setup scripts? export FREESURFER_HOME=<freesurfer_installation_directory>/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh - Josh

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GLUT: Fatal error in tkmedit.bin: visual with necessary capabilities not found
by Kallirroi Retzepis 22 Feb '13

22 Feb '13

Hi all, I am a new student at the Martinos and very new to the freesurfer community - I am actually in the learning process for the moment. Today after passing the tkmedit command I keep getting the following message: "GLUT: Fatal error in tkmedit.bin: visual with necessary capabilities not found." This is bizarre since I have been perfectly able to use tkmedit and tksurfer previously. I am using CentOS 6.3. Any suggestions are more than welcome! Kalli

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[Fwd: Re: tkregister2 window error: Remote login]
by zkaufman＠nmr.mgh.harvard.edu 22 Feb '13

22 Feb '13

cc'ing the freesurfer list so other with the same issue may reference. ---------------------------- Original Message ---------------------------- Subject: Re: [Freesurfer] tkregister2 window error: Remote login From: "Sudhin A. Shah" <sut2006(a)med.cornell.edu> Date: Fri, February 22, 2013 10:51 am To: "zkaufman(a)nmr.mgh.harvard.edu" <zkaufman(a)nmr.mgh.harvard.edu> -------------------------------------------------------------------------- Thank you!! This worked :) On Feb 22, 2013, at 10:14 AM, "zkaufman(a)nmr.mgh.harvard.edu" <zkaufman(a)nmr.mgh.harvard.edu> wrote: > Hello Sudhin, > > From what I can tell, it appears that is it possible you have a > compatibility issue between Exceed OpenGL and Mesa GLX (and thus not > directly a freesurfer issue). > > It turns out if your system's libGL.so library is provided by Mesa > 7.1 or later, OpenGL applications will not run remotely. Can you try to > run 'glxinfo' at the command line...? Do you get an error? If so try > setting the environment variable: > > (example using bash) > export LIBGL_ALWAYS_INDIRECT=y > > And then try running tkregister again. Hopefully this works > > -Zeke > > >> Hello, >> >> I am remotely logged in to my Ubuntu system(from Mac). I have previously >> run tkregister2 but am now having trouble; >> >> Opening window subj >> Window type not found >> register: tkoinitwindow(name) failed. >> >> Is there a solution to this? >> >> Thanks, >> >> S >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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longitudinal sulci depth change
by O'Shea,Andrew 22 Feb '13

22 Feb '13

Hello, I was wondering if I could get some clarification regarding the longitudinal measure of rate of change in sulci depth. In our study we have a patient population that participated in an intervention and a similar group of wait list controls. We have scans for pre and post intervention timepoints. I have ran the longitudinal analysis in QDEC looking at the thickness change measures, however I was also interested in the sulc measures. I was able to get the analysis to run with the new measures long.sulc-rate etc. However I am having a hard time conceptualizing the meaning of the results. Does a negative rate change indicate either a deepening or a shallowing of the sulci? Is the opposite the case for gyral regions? Any advice would be greatly appreciated. -Andrew

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Re: [Freesurfer] talairach transformation troubleshooting problem
by Rongxiang Tang 22 Feb '13

22 Feb '13

Hi Bruce, > > Just want to follow up on the error issue: > > It seems that using the stable version for two of the subjects will always give incomplete surface output....and if using the dev version, it seems to require updating the entire binaries to avoid the error. > > I was thinking that if it is ok to use stable version for most of the subjects and use dev version for the two subjects that have problems, and finally run group analysis with the whole data set? > > Thanks, > Catherine > > > > > On Feb 19, 2013, at 10:32 AM, Rongxiang Tang <rongxiangtang(a)yahoo.com> wrote: > >> I have total of 46 subjects with pre and post scans....44 subjects were OK using the stable version. >> >> Catherine >> >> >> From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> To: Rongxiang Tang <rongxiangtang(a)yahoo.com> >> Cc: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu>; Zeke Kaufman <zkaufman(a)nmr.mgh.harvard.edu> >> Sent: Tuesday, February 19, 2013 10:27 AM >> Subject: Re: [Freesurfer] talairach transformation troubleshooting problem >> >> oh, we had this problem briefly. Maybe the .m3z format changed? Can't >> remember. How many subjects do you have? >> >> On Tue, 19 Feb 2013, Rongxiang Tang wrote: >> >> > Hi Bruce, >> > >> > The error is : >> > >> > #@# SubCort Seg Tue Feb 19 03:30:54 EST 2013 >> > >> > mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z >> > /home/virtualuser/apps/freesurfer/average/RB_all_2008-03-26.gca >> > aseg.auto_noCCseg.mgz >> > >> > MatrixAsciiReadFrom: could not scanf parms >> > renormalizing sequences with structure alignment, equivalent to: >> > -renormalize >> > -renormalize_mean 0.500 >> > -regularize 0.500 >> > not handling expanded ventricles... >> > reading 1 input volumes... >> > reading classifier array from >> > /home/virtualuser/apps/freesurfer/average/RB_all_2008-03-26.gca... >> > reading input volume from norm.mgz... >> > average std[0] = 6.9 >> > reading transform from transforms/talairach.m3z... >> > zcat transforms/talairach.m3z >> > Segmentation fault >> > Linux FreeSurfer 2.6.28-19-generic #66-Ubuntu SMP Sat Oct 16 17:39:04 UTC >> > 2010 i686 GNU/Linux >> > >> > recon-all -s 1452 exited with ERRORS at Tue Feb 19 03:31:25 EST 2013 >> > >> > Thanks, >> > Catherine >> > >> > >> > ____________________________________________________________________________ >> > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> > To: Rongxiang Tang <rongxiangtang(a)yahoo.com> >> > Cc: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu>; Zeke Kaufman >> > <zkaufman(a)nmr.mgh.harvard.edu> >> > Sent: Tuesday, February 19, 2013 9:02 AM >> > Subject: Re: [Freesurfer] talairach transformation troubleshooting problem >> > >> > Hi Catherine >> > >> > you need to tell us what the error is. The command line you specify below >> > will run autorecon2 since you told it to. Try -make all instead of the rest >> > and see if it works. It's supposed to only recreate what is needed. >> > >> > cheers >> > Bruce >> > >> > On Tue, 19 Feb 2013, Rongxiang Tang wrote: >> > >> > > Hi Nick, >> > > >> > > The new downloads worked, however I ran into some new problems.... >> > > I only replaced the three binaries and when I ran autorecon2, there is >> > > always error message with mri_rmneck...so I replaced that binary with the >> > > dev version and the error disappeared. But then for the subsequent steps I >> > > ran into more error. >> > > My guess is that I have to replace all binaries with the dev version? My >> > > worry is that since there are only four subjects that need the dev version >> > > to run, and the rest of the subjects were all proceesed with the stable >> > > v.5.0.0...would updating all binaries to the dev version cause >> > inconsistency >> > > with the results? >> > > >> > > another question about the command line...since the recon-all was killed >> > at >> > > mri_rmneck...if I want to rerun the analysis right from where it was >> > > stopped, how do i do that? >> > > I have tried to use recon-all -rmneck -autorecon2 -autorecon3....but >> > somehow >> > > it just ran from the beginning of autorecon2... >> > > >> > > Thanks, >> > > Catherine >> > > >> > > >> > >___________________________________________________________________________ >> > _ >> > > From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> >> > > To: Rongxiang Tang <rongxiangtang(a)yahoo.com> >> > > Cc: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>; Zeke Kaufman >> > > <zkaufman(a)nmr.mgh.harvard.edu> >> > > Sent: Sunday, February 17, 2013 10:26 AM >> > > Subject: Re: [Freesurfer] talairach transformation troubleshooting problem >> > > >> > > for the virtual box ubuntu, you'll want the centos4 build (not the >> > > centos4_x86_64 build, which is 64b). >> > > >> > > Nick >> > > >> > > >> > > > Hi Bruce, >> > > > >> > > > Thanks for the advice. I'm running the recon-all with the new files... >> > > > About updating the binaries...I'm currently using the VirtualBox Ubuntu >> > > > 32b on windows to run the analysis. The version of free surfer I'm using >> > > > is v5.0.0. I actually downloaded the >> > > > freesurfer-Linux-centos4_x86_64-dev.tar.gz from the website, and update >> > > > the 3 binaries you mentioned...however when I ran the recon-all, the >> > > > terminal notifies me that these three binaries file are not executable. >> > > > >> > > > I was wondering if I need to update the entire binaries? >> > > > >> > > > Thank you, >> > > > Catherine >> > > > >> > > > >> > > > >> > > > ________________________________ >> > > > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> > > > To: Rongxiang Tang <rongxiangtang(a)yahoo.com> >> > > > Cc: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu>; Zeke Kaufman >> > > > <zkaufman(a)nmr.mgh.harvard.edu> >> > > > Sent: Friday, February 15, 2013 5:04 PM >> > > > Subject: Re: [Freesurfer] talairach transformation troubleshooting >> > problem >> > > > >> > > > Hi Catherine >> > > > >> > > > I'm not entirely sure what went wrong, but running the current dev >> > > > versions of mri_em_register/mri_ca_normalize/mri_ca_register fixes the >> > > > problem. I'll attach the relevant files. Put the talairach.lta and >> > > > talairach.xfm in the mri/transforms dir, and the norm.mgz and >> > > > aseg.auto_noCCseg.mgz in the mri dir, and try running recon-all -make >> > all >> > > > -s <subject name> >> > > > >> > > > actually the talairach.m3z is too big. Maybe the best thing to do is to >> > > > update your binaries and try it with the new ones and see if that fixes >> > it >> > > > for you. What hardware/software env are you using? Nick or Zeke can get >> > > > you the right versions. I'll filedrop the .m3z >> > > > >> > > > cheers >> > > > Bruce >> > > > >> > > > >> > > > On Thu, 14 Feb 2013, Rongxiang Tang wrote: >> > > > >> > > >> Hi Bruce, >> > > >> >> > > >> The aseg is also problematic for several slices....I uploaded the >> > > >> subject dir on the Matinos center file drop...since the >> > > >> file is too big, I separated into two parts. >> > > >> >> > > >> Thanks, >> > > >> Catherine >> > > >> >> > >>>_________________________________________________________________________ >> > __ >> > > ________________________________________________ >> > > >> From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> > > >> To: Rongxiang Tang <rongxiangtang(a)yahoo.com> >> > > >> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >> > > >> Sent: Thursday, February 14, 2013 2:42 PM >> > > >> Subject: Re: [Freesurfer] talairach transformation troubleshooting >> > > >> problem >> > > >> >> > > >> probably not, although it's hard to say. If you upload the whole >> > subject >> > > >> dir I'll take a look. How does the aseg look? >> > > >> On Thu, 14 Feb 2013, Rongxiang Tang wrote: >> > > >> >> > > >> > Hi Bruce, >> > > >> > >> > > >> > I checked the skullstrip stage using this command: >> > > >> > >> > > >> > tkmedit subjectid brainmask.mgz -aux T1.mgz -surfs.... >> > > >> > and both of the brainmask and T1 images look fine.... the wm.mgz is >> > > >> problema >> > > >> > tic, with some area missing..... I was wondering if I need to >> > manually >> > > >> adding control points to solve the pro >> > > >> > blem. >> > > >> > Thanks, >> > > >> > Catherine >> > > >> > >> > > >>>__________________________________________________________________________ >> > _ >> > > _ >> > > >> > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> > > >> > To: Rongxiang Tang <rongxiangtang(a)yahoo.com> >> > > >> > Sent: Thursday, February 14, 2013 2:03 PM >> > > >> > Subject: Re: [Freesurfer] talairach transformation troubleshooting >> > > >> problem >> > > >> > >> > > >> > Hi Catherine >> > > >> > >> > > >> > that looks like something went wrong in the surface recon, not in the >> > > >> > talairaching. Maybe a skullstrip problem? You need to investigate. >> > > >> Also, >> > > >> > please cc the list so that others can answer! >> > > >> > >> > > >> > thanks >> > > >> > Bruce >> > > >> > On Thu, 14 Feb 2013, Rongxiang Tang wrote: >> > > >> > >> > > >> > > Hi Bruce, >> > > >> > > >> > > >> > > I attached two images...one is the target view and the other is the >> > > >> > moveable >> > > >> > > view. >> > > >> > > >> > > >> > > Thanks, >> > > >> > > Catherine >> > > >> > > >> > > >> > > >> > > >>>>_________________________________________________________________________ >> > _ >> > > _ >> > > >> > _ >> > > >> > > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> > > >> > > To: Rongxiang Tang <rongxiangtang(a)yahoo.com> >> > > >> > > Cc: "freesurfer(a)nmr.mgh.harvard.edu" >> > > >> <freesurfer(a)nmr.mgh.harvard.edu> >> > > >> > > Sent: Thursday, February 14, 2013 1:33 PM >> > > >> > > Subject: Re: [Freesurfer] talairach transformation troubleshooting >> > > >> problem >> > > >> > > >> > > >> > > Hi Catherine >> > > >> > > >> > > >> > > can you send us an image of what you are looking at? >> > > >> > > >> > > >> > > thanks >> > > >> > > Bruce >> > > >> > > On Thu, 14 Feb 2013, >> > > >> > > Rongxiang Tang wrote: >> > > >> > > >> > > >> > > > Dear All, >> > > >> > > > >> > > >> > > > When I was checking the talairach transformation output, I >> > noticed >> > > >> that >> > > >> > > some of the white matter was not included inside >> > > >> > > > the green line. Instead of drawing the green line to include all >> > > >> of the >> > > >> > > white matter of the whole brain, it somehow only >> > > >> > > > includes the bottom half of the white matter of the brain. >> > > >> > > > >> > > >> > > > Is there a way to fix that? >> > > >> > > > >> > > >> > > > Thanks, >> > > >> > > > Catherine >> > > >> > > > >> > > >> > > > >> > > >> > > >> > > >> > > >> > > >> > > 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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tkregister2 window error: Remote login
by Sudhin A. Shah 22 Feb '13

22 Feb '13

Hello, I am remotely logged in to my Ubuntu system(from Mac). I have previously run tkregister2 but am now having trouble; Opening window subj Window type not found register: tkoinitwindow(name) failed. Is there a solution to this? Thanks, S

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Possible thresholding bug with automatic labeling of V1 using the Hinds method
by Axel Kohler 22 Feb '13

22 Feb '13

Dear Freesurfers, I came across a possible issue during the automatic labeling of V1 using the Hinds method (http://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps) If you use the command "recon-all -s subjid -label_v1", as far as I can see, mainly the shell script "predict_v1.sh" in $FREESURFER_HOME/bin is executed. Apart from the fact whether you have a FreeSurfer version in which the command runs smoothly or whether you have to use a workaround combining different FreeSurfer versions described by Krish Singh (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20363.html) you should be careful with the automatically generated thresholded label files "lh.v1.predict.label" and "rh.v1.predict.label". Note already here that the basic output of the analysis (rh.v1.prob.label/lh.v1.prob.label) is not affected by this. It is only relevant when you use the thresholding function "threshold_labelfile_at_0p8", which is included in "predict_v1.sh" or has been cited separately by Krish Singh in an e-mail post (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20367.html) (1) The first problem people might run into is not pernicious and probably depends on the exact shell version you are using. I had a problem with the following line in threshold_labelfile_at_0p8 (didn't run in tcsh OR bash): numlab=`wc -l /tmp/tmpthreshout | sed "s/ .*$//"` It is supposed to compute the number of vertices, which is printed on the second line of the label file. Since the command does not succeed with current shell versions, the second line remains empty and if you load the label, it is shown not at all or in a distorted fashion. An easy replacement that should work is: numlab=`wc -l < /tmp/tmpthreshout` (2) The second problem gives you wrong results randomly in at least some cases (haven't tested the generality). The line: cat $infile | sed "/^#/d;/^[0-9]*$/d;/.* 0\\.[0-7].*$/d" \ > /tmp/tmpthreshout throws out lines with probability values (which are in the last column) below 0.8 with the sed part "/.* 0\\.[0-7].*$/d". Unfortunately, the regular expression also picks up coordinate values in other columns that might start with 0.x, so you end up with fewer vertices than you should have. In most cases, it won't severely affect your results, because not many vertices are thrown out in this way. But it's an error and might also be different for the different hemispheres. (In one case, I had 20-30 dropouts only in the left hemisphere.) A replacement for the line of code would be, e.g.: cat $infile | sed "/^#/d;/^[0-9]*$/d;/.* 0\\.[0-7]0\{5\}$/d" \ > /tmp/tmpthreshout Or you use something more sophisticated on columns (awk?). Maybe someone could confirm the bug. It would be nice if it could be changed in future versions. Obviously, there is also no effect for the GUI thresholding function. So if you do all your thresholding manually from the "prob" file, that's fine. Best regards, Axel Kohler -- =================================================================== Axel Kohler, PhD University of Münster Institute of Psychology Fliednerstr. 21 D-48149 Münster - GERMANY - phone: +49 (251) 83-34181 e-mail: axel.kohler(a)uni-muenster.de web: http://www.axel-kohler.de ===================================================================

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Art of Neuroscience competition 2013 - Call for submissions
by Martijn Steenwijk 22 Feb '13

22 Feb '13

*Art of Neuroscience competition 2013 - Call for submissions* The Art of Neuroscience competition is held every year on the occasion of the Brain Awareness week. European neuroscientists are invited to submit *their most striking images and videos depicting their work*. At the yearly Art of Neuroscience event, a seminar is held and prizes are awarded for the best submissions. This year’s event will be held on March 13th, 2013 from 15.00-18.00 at the Eye film institute in Amsterdam, the Netherlands. The Art of Neuroscience competition 2013 is now open to all *European residents* doing neuroscientific research. We are looking for beautiful imagery and videos depicting your work or a neuroscientific concept. Two Google tablets will be awarded. One in the category best image, and one in the category best video submissions. Participants need to register with their institution e-mails. Check the section “Get started!” for all rules and regulations on our website: http://aon.herseninstituut.knaw.nl. *The deadline for submissions is March 1, 2013 5PM GMT*. Winners will be announced at the Art of Neuroscience event on March 13, 2013 in Amsterdam and need to arrange their own travel arrangements in order to attend the seminar and award ceremony.

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mri_vol2vol call
by Gregory Kirk 21 Feb '13

21 Feb '13

Hi I found my old notes ( re my message earlier) I think this is now correct for mapping subject 822 FA onto my template 816, I know the cvs technology is recent, so just asking to make sure there is now a newer/prefered way. mri_vol2vol --targ /study5/aa-scratch/TEENEMO/twins_freesurfer/816/mri/norm.mgz --m3z /study5/aa-scratch/TEENEMO/twins_freesurfer/822/cvs/combined_to816_elreg_afteraseg-norm.m3z --noDefM3zPath --reg /study5/aa-scratch/TEENEMO/twins_tracula/recons/822/dmri/xfms/anatorig2diff.bbr.dat --mov /study5/aa-scratch/TE ENEMO/twins_tracula/recons/822/dmri/dtifit_FA.nii.gz --o /study5/aa-scratch/TEENEMO/twins_freesurfer/822/cvs/FA.mgz --no-save-reg done thanks

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Help with the error info: mghRead subject/surf/lh.inflated.H, could not open file
by Xiaowei Song 21 Feb '13

21 Feb '13

Dear Bruce and freesurfer experts, I am trying to use mri_average_subjects, but encountered the error: mghRead(/fullpath/surf/lh.inflated.H, -1): could not open file. . Then I tried mri_info subject/surf/lh.inflated.H , and it worked. But when I tried mri_info $(readlink -f subject/surf/lh.inflated.H) , the same error information is told. Besides, I tried the same command to the downloaded buckner_data and no error happened. How to fix this? The following information is from bugr: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: Red Hat Enterprise Linux Server release 6.3 (Santiago) Kernel info: Linux 2.6.32-279.22.1.el6.x86_64 x86_64 Thanks -- Xiaowei Song

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