Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

license file
by Frederick Klauschen 31 Aug '06

31 Aug '06

Hi, I have difficulties registering and obtaining a license file. On the page: https://surfer.nmr.mgh.harvard.edu/fswiki/Registration clicking on the link: "Follow this link to obtain a license key" http://surfer.nmr.mgh.harvard.edu:631/printersregistration.html gives me an access denied message. Frederick __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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mritotal.log
by Chacko Cherian 30 Aug '06

30 Aug '06

Hello all, I wanted to know where the mritotal.log file is created.I checked the /scripts directory but couldnt find it there. I'd like to have a look at the Final objective function value for the subjects I'm running. Thanks in advance Chacko Cherian.

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thickness standard deviation
by Sasha Wolosin 30 Aug '06

30 Aug '06

Dear all, I am interested in measuring mean thickness within ROI in MPRAGEs of children. My mean thickness values tend to be around 3.3 mm, with a standard deviation of about 1mm. I am concerned that these standard deviations are somewhat high. What typical values should I be expecting for standard deviation? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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FSL to FsFast: registration problem
by Paymon Hosseini 30 Aug '06

30 Aug '06

Hi I used both FSL and FsFast to process a set of fMRI data. after using FSL, I used "reg-feat2anat --feat xxxx.feat --subject xxxx" to check the fMRI to T1 registration in FSL. for some reason, I cannot get the FSL registration to come close to the one done by FsFast (please look at figure at http://web.mit.edu/paymon/www/regis.pdf) the left most figure, shows the fMRI to t1epi to T1 registration done entirely in FsFast using "autoreg-sess". the two right most figures, show registrations done in FSL followed by "reg-feat2anat --feat xxxx.feat --subject xxxx". Visually, the registration done with FsFast looks much better than the ones done with FSL and then transformed to FsFast. here is my question: should I be suspicious of the my registration process in FSL, or am I not applying reg-feat2anat correctly, and hence causing a poor fMRI to T1 registration. I am using FSL 3.3.7, and FsFast under nmrenv. thanks a lot for your help, paymon

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Regarding missing DICOM fields
by Niels Bergsland 29 Aug '06

29 Aug '06

Hi, We have some old scans that were originally in ACR-NEMA format which we have converted to DICOM. The problem is that they are missing both the ImagePositionPatient and ImageOrientationPatient fields. Is there anyway to use freesurfer without having these two fields? Based on the post by Doug which I found at http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03409.html , I am afraid not... Thank you for any help. Regards, Niels Bergsland

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Re: [Freesurfer] tkmedit crashes/freezes
by Derin Cobia 29 Aug '06

29 Aug '06

Bruce, No, I processed all of them the same way (converted files, -autorecon1, etc). The scan quality differs among them, but I tossed the really bad ones. Here is the xdebug file. Also, is what I'm seeing in this slice (see attached jpg) something to worry about? If I scroll through other slices, then come back to it, the artifacts are gone. This happens randomly on various slices on some of the subjects, but it never stays. I have updated the drivers for the video card, and haven't had any issues (yet). I'll keep my eye on it. Thanks for your help. -Derin > were these processed any differently? The .xdebug_tkmedit should be in pwd > wherever you ran it from. > > Bruce > > > On Tue, 29 Aug 2006, Derin Cobia > wrote: > >> Kevin- >> Yeah, either way. In my "infinite" wisdom I thought that scrolling >> slower >> would help, but not so. >> >> Nick- >> I'm unable to locate a .xdebug_tkmedit file in either the freesurfer or >> subjects directory. Would it be somewhere else? It looks like we're >> using the 1.0-8178 Nvidia driver for our Quadro FX card, but their site >> shows a 1.0-8762 as the latest. I'll see if we can update it today, >> maybe >> that will help. >> >> On the side... why are my intensity values "infinite" for the following >> subject? I've briefly checked brainmask.mgz, and differing intensities >> appear. Any ideas? Thanks. >> >> -Derin >> >> #-------------------------------------------- >> #@# WM Segmentation Mon Aug 28 04:00:48 CDT 2006 >> >> mri_segment brain.mgz wm.seg.mgz >> >> doing initial intensity segmentation... >> using local statistics to label ambiguous voxels... >> computing class statistics for intensity windows... >> WM: nan +- nan [100000.0 --> -100000.0] >> GM: nan +- nan [100000.0 --> -100000.0] >> mri_segment: class statistics not finite - check input volume! >> Linux gizmo 2.6.9-11.ELsmp #1 SMP Wed Jun 8 17:54:20 CDT 2005 i686 i686 >> i386 GNU/Linux >> >> recon-all exited with ERRORS at Mon Aug 28 04:00:54 CDT 2006 >> >> >>> Hm, I can't reproduce this. >>> >>> So, you load up a volume, and repeatedly press an arrow key to scroll >>> through the slices? Or hold the button down? >>> >>> On Mon, Aug 28, 2006 at 11:16:49AM -0500, Derin Cobia wrote: >>>> I've been experiencing some crashes/freezing using tkmedit lately, and >>>> have been able to reproduce it pretty reliably. It occurs when I >>>> scroll >>>> through the slices of the subject either using the arrows keys or >>>> clicking >>>> through on the toolbar. It happens when viewing a variety of volumes >>>> (brainmask, T1, etc), and from a variety of perspectives (coronal, >>>> sagittal, etc); it also happens on different subjects as well. This >>>> occurs no matter what workstation I use in the lab (networked >>>> environment). My X freezes up as well as the keyboard, but the mouse >>>> doesn't. I used to be able to restart my X remotely, but now tkmedit >>>> locks up so bad I have to reboot. Any ideas? >>>> >>>> Dell Precision 670 Workstations >>>> CentOS 4.1 (32-bit) >>>> >>>> -------- freesurfer-Linux-centos4-stable-pub-v3.0.3 -------- >>>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>>> FREESURFER_HOME /pkg/brainmap/freesurfer >>>> FSFAST_HOME /pkg/brainmap/freesurfer/fsfast >>>> SUBJECTS_DIR /disk/k2/freesurfer/neuromorph_v1_flash/ >>>> FUNCTIONALS_DIR /pkg/brainmap/freesurfer/sessions >>>> MINC_BIN_DIR /pkg/brainmap/freesurfer/mni/bin >>>> MINC_LIB_DIR /pkg/brainmap/freesurfer/mni/lib >>>> PERL5LIB /pkg/brainmap/freesurfer/mni/lib/perl5/5.8.0 >>>> GSL_DIR /pkg/brainmap/freesurfer/lib/gsl >>>> QTDIR /usr/lib/qt-3.3 >>>> TCLLIBPATH /pkg/brainmap/freesurfer/lib/tcltktixblt/lib >>>> FSL_DIR /pkg/brainmap/freesurfer/fsl >>>> >>>> [derin@fozzy ~]$ which tkmedit >>>> /pkg/brainmap/freesurfer/bin//tkmedit >>>> >>>> cd /disk/k2/freesurfer/neuromorph_v1_flash/ >>>> >>>> Thanks in advance. >>> >>> >>> -- >>> Kevin Teich >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >

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Re: [Freesurfer] tkmedit crashes/freezes
by Derin Cobia 29 Aug '06

29 Aug '06

Sorry, visual artifacts- yes (still there), crashing/freezing- no (but I've been trying hard). It's only been about an hour since the update, I'll keep you posted. So, should I worry about the artifacts affecting output? If I scroll through the slices long enough, they eventually all disappear. -Derin > OK, so since you updated the graphics driver, you've had no problems > with either the visual artifacts or the crashing/freezing? If there > have been no problems, we'll assume the graphics driver fixed > it. Otherwise, let us know. > > On Tue, Aug 29, 2006 at 01:24:09PM -0500, Derin Cobia wrote: >> Bruce, >> >> No, I processed all of them the same way (converted files, -autorecon1, >> etc). The scan quality differs among them, but I tossed the really bad >> ones. Here is the xdebug file. Also, is what I'm seeing in this slice >> (see attached jpg) something to worry about? If I scroll through other >> slices, then come back to it, the artifacts are gone. This happens >> randomly on various slices on some of the subjects, but it never stays. >> >> I have updated the drivers for the video card, and haven't had any >> issues >> (yet). I'll keep my eye on it. Thanks for your help. >> >> -Derin >> >> > were these processed any differently? The .xdebug_tkmedit should be in >> pwd >> > wherever you ran it from. >> > >> > Bruce >> > >> > >> > On Tue, 29 Aug 2006, Derin Cobia >> > wrote: >> > >> >> Kevin- >> >> Yeah, either way. In my "infinite" wisdom I thought that scrolling >> >> slower >> >> would help, but not so. >> >> >> >> Nick- >> >> I'm unable to locate a .xdebug_tkmedit file in either the freesurfer >> or >> >> subjects directory. Would it be somewhere else? It looks like we're >> >> using the 1.0-8178 Nvidia driver for our Quadro FX card, but their >> site >> >> shows a 1.0-8762 as the latest. I'll see if we can update it today, >> >> maybe >> >> that will help. >> >> >> >> On the side... why are my intensity values "infinite" for the >> following >> >> subject? I've briefly checked brainmask.mgz, and differing >> intensities >> >> appear. Any ideas? Thanks. >> >> >> >> -Derin >> >> >> >> #-------------------------------------------- >> >> #@# WM Segmentation Mon Aug 28 04:00:48 CDT 2006 >> >> >> >> mri_segment brain.mgz wm.seg.mgz >> >> >> >> doing initial intensity segmentation... >> >> using local statistics to label ambiguous voxels... >> >> computing class statistics for intensity windows... >> >> WM: nan +- nan [100000.0 --> -100000.0] >> >> GM: nan +- nan [100000.0 --> -100000.0] >> >> mri_segment: class statistics not finite - check input volume! >> >> Linux gizmo 2.6.9-11.ELsmp #1 SMP Wed Jun 8 17:54:20 CDT 2005 i686 >> i686 >> >> i386 GNU/Linux >> >> >> >> recon-all exited with ERRORS at Mon Aug 28 04:00:54 CDT 2006 >> >> >> >> >> >>> Hm, I can't reproduce this. >> >>> >> >>> So, you load up a volume, and repeatedly press an arrow key to >> scroll >> >>> through the slices? Or hold the button down? >> >>> >> >>> On Mon, Aug 28, 2006 at 11:16:49AM -0500, Derin Cobia wrote: >> >>>> I've been experiencing some crashes/freezing using tkmedit lately, >> and >> >>>> have been able to reproduce it pretty reliably. It occurs when I >> >>>> scroll >> >>>> through the slices of the subject either using the arrows keys or >> >>>> clicking >> >>>> through on the toolbar. It happens when viewing a variety of >> volumes >> >>>> (brainmask, T1, etc), and from a variety of perspectives (coronal, >> >>>> sagittal, etc); it also happens on different subjects as well. >> This >> >>>> occurs no matter what workstation I use in the lab (networked >> >>>> environment). My X freezes up as well as the keyboard, but the >> mouse >> >>>> doesn't. I used to be able to restart my X remotely, but now >> tkmedit >> >>>> locks up so bad I have to reboot. Any ideas? >> >>>> >> >>>> Dell Precision 670 Workstations >> >>>> CentOS 4.1 (32-bit) >> >>>> >> >>>> -------- freesurfer-Linux-centos4-stable-pub-v3.0.3 -------- >> >>>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> >>>> FREESURFER_HOME /pkg/brainmap/freesurfer >> >>>> FSFAST_HOME /pkg/brainmap/freesurfer/fsfast >> >>>> SUBJECTS_DIR /disk/k2/freesurfer/neuromorph_v1_flash/ >> >>>> FUNCTIONALS_DIR /pkg/brainmap/freesurfer/sessions >> >>>> MINC_BIN_DIR /pkg/brainmap/freesurfer/mni/bin >> >>>> MINC_LIB_DIR /pkg/brainmap/freesurfer/mni/lib >> >>>> PERL5LIB /pkg/brainmap/freesurfer/mni/lib/perl5/5.8.0 >> >>>> GSL_DIR /pkg/brainmap/freesurfer/lib/gsl >> >>>> QTDIR /usr/lib/qt-3.3 >> >>>> TCLLIBPATH /pkg/brainmap/freesurfer/lib/tcltktixblt/lib >> >>>> FSL_DIR /pkg/brainmap/freesurfer/fsl >> >>>> >> >>>> [derin@fozzy ~]$ which tkmedit >> >>>> /pkg/brainmap/freesurfer/bin//tkmedit >> >>>> >> >>>> cd /disk/k2/freesurfer/neuromorph_v1_flash/ >> >>>> >> >>>> Thanks in advance. >> >>> >> >>> >> >>> -- >> >>> Kevin Teich >> >>> >> >> >> >> _______________________________________________ >> >> 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 >> >> > > -- > Kevin Teich >

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Can I use MRI corregistered PET functional data instead of fmri?
by jorge luis 29 Aug '06

29 Aug '06

Hello all How can I use corregistered PET functional data instead of fmri to overlay freesurfer's anatomical volumes and surfaces? Some tips are welcome Thank you in advance Jorge ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

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Re: [Freesurfer] tkmedit crashes/freezes
by Derin Cobia 29 Aug '06

29 Aug '06

Kevin- Yeah, either way. In my "infinite" wisdom I thought that scrolling slower would help, but not so. Nick- I'm unable to locate a .xdebug_tkmedit file in either the freesurfer or subjects directory. Would it be somewhere else? It looks like we're using the 1.0-8178 Nvidia driver for our Quadro FX card, but their site shows a 1.0-8762 as the latest. I'll see if we can update it today, maybe that will help. On the side... why are my intensity values "infinite" for the following subject? I've briefly checked brainmask.mgz, and differing intensities appear. Any ideas? Thanks. -Derin #-------------------------------------------- #@# WM Segmentation Mon Aug 28 04:00:48 CDT 2006 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM: nan +- nan [100000.0 --> -100000.0] GM: nan +- nan [100000.0 --> -100000.0] mri_segment: class statistics not finite - check input volume! Linux gizmo 2.6.9-11.ELsmp #1 SMP Wed Jun 8 17:54:20 CDT 2005 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Mon Aug 28 04:00:54 CDT 2006 > Hm, I can't reproduce this. > > So, you load up a volume, and repeatedly press an arrow key to scroll > through the slices? Or hold the button down? > > On Mon, Aug 28, 2006 at 11:16:49AM -0500, Derin Cobia wrote: >> I've been experiencing some crashes/freezing using tkmedit lately, and >> have been able to reproduce it pretty reliably. It occurs when I scroll >> through the slices of the subject either using the arrows keys or >> clicking >> through on the toolbar. It happens when viewing a variety of volumes >> (brainmask, T1, etc), and from a variety of perspectives (coronal, >> sagittal, etc); it also happens on different subjects as well. This >> occurs no matter what workstation I use in the lab (networked >> environment). My X freezes up as well as the keyboard, but the mouse >> doesn't. I used to be able to restart my X remotely, but now tkmedit >> locks up so bad I have to reboot. Any ideas? >> >> Dell Precision 670 Workstations >> CentOS 4.1 (32-bit) >> >> -------- freesurfer-Linux-centos4-stable-pub-v3.0.3 -------- >> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> FREESURFER_HOME /pkg/brainmap/freesurfer >> FSFAST_HOME /pkg/brainmap/freesurfer/fsfast >> SUBJECTS_DIR /disk/k2/freesurfer/neuromorph_v1_flash/ >> FUNCTIONALS_DIR /pkg/brainmap/freesurfer/sessions >> MINC_BIN_DIR /pkg/brainmap/freesurfer/mni/bin >> MINC_LIB_DIR /pkg/brainmap/freesurfer/mni/lib >> PERL5LIB /pkg/brainmap/freesurfer/mni/lib/perl5/5.8.0 >> GSL_DIR /pkg/brainmap/freesurfer/lib/gsl >> QTDIR /usr/lib/qt-3.3 >> TCLLIBPATH /pkg/brainmap/freesurfer/lib/tcltktixblt/lib >> FSL_DIR /pkg/brainmap/freesurfer/fsl >> >> [derin@fozzy ~]$ which tkmedit >> /pkg/brainmap/freesurfer/bin//tkmedit >> >> cd /disk/k2/freesurfer/neuromorph_v1_flash/ >> >> Thanks in advance. > > > -- > Kevin Teich >

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Re: Freesurfer Digest, Vol 30, Issue 26
by Sebastian Moeller 28 Aug '06

28 Aug '06

Hi Doug, On 28. Aug 2006, at 23:55 Uhr, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Date: Mon, 28 Aug 2006 17:53:30 -0400 > From: Doug Greve <greve(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] Re: newbie question event-related > To: Sebastian Moeller <sebastian.moeller(a)lur.rwth-aachen.de> > Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <44F365DA.1040805(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Sebastian, > > are you using an FIR or gammafit? Gammafit (-gammafit 0 1.25 -gammaexp 2 in union with -taumax 20 and -dt event-related). To illustrate this, I used the same parameters with "-dt blocked", but my new paradigm is so sparse (200ms timulation every 16 seconds), that event related analysis seems like a good idea. Since we are at it ;), am I right that I should set the TER to 0.2000 and my stimulation epochs to one, while the only fixation periods are set to zero? Ahoi & Thanks Sebastian > > doug > > Sebastian Moeller wrote: > >> Hi List, hi Doug, >> >> for the first time I have now data, that realloy wants event-related >> analysis (200ms stimulation every 10 seconds). Now, using a TER of 0.2 >> in the para-file and using "-dt event-related" in mkanalysis-sess.new >> (3.0.3 pub x86_64 centos4) was the easy part, but what do I have to >> specify in mkcontast-sess? Especially thi "-ircorr" complex (with >> -deltarang and -taurange) is daunting. Is it necessary to specify >> anything here to get a real event-related analysis, or does fs-fast >> already know enough without these parameters (as I specified delta, >> tau and even taummax in mkanalysis)? So far any nicorr value I used >> produced errors on the way... >> I would be delighted for any pointer of how to properly convinve >> fs-fast to analyse my data ;). >> >> Ahoi & thanks >> Sebastian > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > ------------------------------ > -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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