Freesurfer August 2006

freesurfer@nmr.mgh.harvard.edu

48 participants
74 discussions

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

2 4

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 >> >> >> >

3 2

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 >

1 0

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

3 2

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 >

2 1

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

2 2

newbie question event-related
by Sebastian Moeller 28 Aug '06

28 Aug '06

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 -- 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

3 2

tkmedit crashes/freezes
by Derin Cobia 28 Aug '06

28 Aug '06

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. -Derin

3 2

nii header info
by Najmeh Khalili M. 28 Aug '06

28 Aug '06

Hello, I was wondering if there is a command that dumps the header information of .nii file. Also, does mri_convert transfer dti acquisition parameters (b-value, directions) from the DICOM to nifti? (Our dti sequence does write its parameters to the DICOM file.) Any pointer's appreciated. cheers, Naj

3 2

questions about group analysis
by Ray Fix 27 Aug '06

27 Aug '06

Hello, I have some questions about doing group analysis. I know these are really basic... but everyone loves easy softballs, right? Question 1. How should I define multiple classes? The tutorial examples show two classes, male and female. If I have patient and controls, in addition to male and female, should I define it : class Patient class Control class Male class Female Variable Age Input subject1 Patient Male 24 Input subject2 Control Female 39 : or do I have to boil it down to one column?? class PatientFemale class PatientMale class ControlFemale class ControlMale Variable Age Input subject1 PatientMale 24 Input subject2 ControlFemale 39 : or should I separate these into different FSGD files? or some other way? Question 2: Best practice for a small study If I have lots of slopes, but not so many samples (<50), is it advisable to make one big FSFD file or make several small FSGD files with all those slopes? Question 3: DOSS versus DODS By staring at Doug Greve's excellent slides http:// surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsgroupana.pdf I was able to figure out whad doss and dods do the design matrix. Can someone make a simple statement as when to use one instead of the other? Question 4: Multiple Comparison Section 4 of the tutorial gets into multiple comparison. I started to run the sample and realized it will probably take my computer 3 years to finish executing ;) Can someone tell me what problem this is solving for me? What is multiple comparison and where do you run into trouble by not doing it? That's all I can think of for now. Thank you. Ray PS: I did notice there is a broken link in the wiki tutorial. On the page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ GroupAnalysis there is a link in section 3.0 that points to information about creating contrast vectors. It is broken. I think it should point to: https://surfer.nmr.mgh.harvard.edu/fswiki/ FsTutorial_2fCreateContrastVectors

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer August 2006