Freesurfer May 2009

freesurfer@nmr.mgh.harvard.edu

81 participants
126 discussions

RE: GLUT Error
by Andrew Jahn 14 May '09

14 May '09

Hi again, I have been encountering an error when attempting to use either tksurfer or tkmedit via VNC on a local server. Here is the output whenever I type tkmedit or tksurfer: GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by display: 1.0 I looked through the threads regarding this problem, but still have been unable to find a solution. The output of 'cat /etc/redhat-release' is Red Hat Enterprise Linux WS release r (Nahant Update 7) and here is the output from the command ldd `which tkmedit.bin`: libtix8.1.8.4.so => not found libtk8.4.so => /usr/lib64/libtk8.4.so (0x0000003d43d00000) libtcl8.4.so => /usr/lib64/libtcl8.4.so (0x0000003d43b00000) libGLU.so.1 => /usr/X11R6/lib64/libGLU.so.1 (0x0000003d48300000) libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003d48500000) libXext.so.6 => /usr/X11R6/lib64/libXext.so.6 (0x0000003d44f00000) libX11.so.6 => /usr/X11R6/lib64/libX11.so.6 (0x0000003d44d00000) libXmu.so.6 => /usr/X11R6/lib64/libXmu.so.6 (0x0000003d47900000) libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x0000003d47100000) libtiff.so.3 => /usr/lib64/libtiff.so.3 (0x0000003d4c000000) libz.so.1 => /usr/lib64/libz.so.1 (0x0000003d45100000) libcrypt.so.1 => /lib64/libcrypt.so.1 (0x0000003d48a00000) libdl.so.2 => /lib64/libdl.so.2 (0x0000003d44b00000) libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x0000003d45300000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003d47500000) libm.so.6 => /lib64/tls/libm.so.6 (0x0000003d44900000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003d47300000) libc.so.6 => /lib64/tls/libc.so.6 (0x0000003d44600000) libGLcore.so.1 => /usr/lib64/libGLcore.so.1 (0x0000002a95586000) libnvidia-tls.so.1 => /usr/lib64/tls/libnvidia-tls.so.1 (0x0000003d44400000) libXt.so.6 => /usr/X11R6/lib64/libXt.so.6 (0x0000003d4a100000) libSM.so.6 => /usr/X11R6/lib64/libSM.so.6 (0x0000003d45700000) libICE.so.6 => /usr/X11R6/lib64/libICE.so.6 (0x0000003d45500000) /lib64/ld-linux-x86-64.so.2 (0x0000003d43900000) Also, here is the content of the .xdebug_tkmedit file following an unsuccessful tkmedit command: tkmedit started: Thu May 14 14:55:44 2009 tkmedit.bin $Id: tkmedit.c,v 1.320.2.9 2009/01/27 20:41:02 greve Exp $ $Name: stable4 $ Any help or advice is greatly appreciated in advance. Thanks! -Andrew

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License Key issue (not recognized)
by ozgun ozalay 14 May '09

14 May '09

Hi; I'm Ozgun Ozalay, researcher at Ege University/Turkey. One of my friends recommended FreeSurfer's "mri_convert" program to convert my Siemens .IMA files to a more common format .nii. i've downloaded freesurfer from your wiki pages and made my registration too. i've recieved an e-mail with details of my license. Upon installing "freesurfer" to /home/ozgun/AnV/freesurfer i configured enviroment too as described in wiki with bash shell; /export FREESURFER_HOME=/home/ozgun/freesurfer/ /source $FREESURFER_HOME/SetUpFreeSurfer.sh/ I recieved no errors during this process. /source /home/ozgun/AnV/freesurfer/SetUpFreeSurfer.sh/ /-------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0 --------/ /Setting up environment for FreeSurfer/FS-FAST (and FSL)/ /FREESURFER_HOME /home/ozgun/AnV/freesurfer// /FSFAST_HOME /home/ozgun/AnV/freesurfer//fsfast/ /FSF_OUTPUT_FORMAT nii/ /SUBJECTS_DIR /home/ozgun/AnV/freesurfer//subjects/ /MNI_DIR /home/ozgun/AnV/freesurfer//mni/ /FSL_DIR /home/ozgun/AnV/FSL/fsl/ But when i try to execute "mri_convert" it says my license isn't ok. /ozgun@linux-dkvs:~/AnV/freesurfer/bin> ./mri_convert /home/ozgun/AnV/orn.IMA/ //home/ozgun/orn.nii/ /./mri_convert /home/ozgun/AnV/orn.IMA /home/ozgun/orn.nii/ /$Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $/ /reading from /home/ozgun/AnV/orn.IMA.../ /--------------------------------------------------------------------------/ /ERROR: Invalid FreeSurfer license key found in license file/ //home/ozgun/AnV/freesurfer/.license/ /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./ /--------------------------------------------------------------------------/ / / I created ".license" file in my freesurfer home directory (/home/ozgun/AnV/freesurfer) and pasted 3 lines from your e-mail to this empty document and saved. Also attaching the .license file i've created. Did i do something wrong? By the way, i'm using OpenSuse 11.1 with kernel 2.6.27.21-0.1-default, KDE 4.1 as desktop enviroment. Thanks anyway ;) #---------------CUT HERE--------------- ozgun.ozalay(a)gmail.com 7235 *CZag.N9G9Ekc #---------------CUT HERE---------------

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smoothing with mri_surf2surf
by Gregory Dierksen 14 May '09

14 May '09

Hi, I want to smooth a cortical thickness map using values only in a specific area. Basically I want to mask out all other segmentations, for example smooth with fwhm of 20 only in the postcentral region. I've used quite a few combinations of the -label-src and -label-trg flags and noticed a slight problem: Using the command line (which seems to give the "best" results): mri_surf2surf --hemi rh --s fsaverage --sval ./rh.Input.mgh --fwhm 20 --label-trg ./postcentral.label --tval rh.Output.mgz When the rh.Input.mgh has been masked before running surf2surf using postcentral.label (so only the postcentral region is non-zero), I get DIFFERENT values than if rh.Input.mgh is NOT previously masked by postcentral.label (ie ALL verticies have non-zero values inside and outside postcentral region). How can I get mri_surf2surf (or perhaps some other command) to smooth only within a specified region without taking values from outside this region? Thanks for the help, Greg

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From MNI152 to Subject's space
by Campanella Martina 14 May '09

14 May '09

Hi "Freesurfer", We need to remap a volume in MNI152 to a subject space in order to find the correspondent label... Any suggestion? Cheers, Martina Campanella

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Can fieldsigns be added across sessions?
by Jeff Phillips 14 May '09

14 May '09

Hi all, I would like to add fieldsigns across multiple retinotopy sessions in the same subject, in order to get a metric of the reliability of the mapping. However, when I tried to do this in one subject, I found that fieldsigns from two sessions largely canceled one another out. This led to a discussion in our lab of whether the fieldsign 1) has a consistent meaning across sessions and subjects, or 2) whether the fieldsign in a given region, say V1, may switch from positive to negative due to noise or between-subject differences. For example, a colleague speculated that paint-sess could start with +1 at an arbitrary starting point on the edge of an occipital patch, then flip the sign whenever the polar angle/eccentricity gradients reversed themselves. Thus, V5 might be +1, V4 = -1, V3 = +1, V2 = -1, and V1 would be +1. However, if noise in a given session resulted in a failure to detect V4, then V1 would end up being the opposite fieldsign, -1. Is this correct? If so, then I might be shooting myself in the foot by adding fieldsign maps from different sessions. I would really appreciate any insight about how the fieldsign is assigned, and whether circumstances like the ones I describe could cause it to flip for a given functional region. Thanks, Jeff Phillips

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Re: [Freesurfer] Literature values for cortical thickness
by Bruce Fischl 14 May '09

14 May '09

Hi Falk, we published some values in our Cerebral Cortex paper , but I suspect the effective thickness will vary a bit as a function of pulse sequence, and certainly it will vary with things like age. Rahul has probably tabulated by parcellation unit if that helps. cheers Bruce On Wed, 13 May 2009, Falk Lüsebrink wrote: > Hi everyone, > > > > As I dont do a study in which I compare a group of subjects with some kind > of abnormality with a control group I was looking for literature values for > cortical thickness. The only paper I found which was written by von Economo > et al. in 1925 doing a post-mortem analysis. > > > > Are there any more recent sources available which maybe even cover in-vivo > values for regional cortical thickness? Actually Im looking for average > values across the whole lobes. > > > > Thanks in advance, > > Falk > >

4 3

map label to subjects
by Juranek, Jenifer 13 May '09

13 May '09

Hi, I'm running fsv405 on a 64bit Linux centos5. I have not had much success with using the File - Save Label - Filename within qdec (v1.1). The gui prompt has a default filename set to lh.untitled.label and I am unable to edit that name, but I can write the default filename to the default dir (e.g. /usr/local/fsaverage/label). Similarly, I am unable to use the File-MapLabeltoSubjects option within qdec. A default label name is not provided and I am unable to type something in the gui box field. I have recursively changed permissions for the subjects dir from /usr/local/freesurfer such that I am the owner and chmod to be 770. Is there a simple solution for my user error?

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Re: Literature values for cortical thickness
by Dana W. Moore 13 May '09

13 May '09

Actually, I have also been looking for cortical thickness normative values. We have run our first few research subjects with FreeSurfer (a normal control and several patients with neurodegenerative disorders), and I wanted to see if the thickness values we're getting are in the normal range. I have two papers: Salat et al. (2004) and Fischl & Dale (2000) in Cerebral Cortex. The Fischl and Dale gives average thickness for gyral and sulcal regions. Am I correct to guess that the average gyral and sulcal regions are taken by averaging the individual gyral and sulcal units from the aparc.a2005s.stats files? The Salat et al. article gives a global thickness measure--I was wondering how I would calculate this? Also, if thickness values are available for individual parcellation units and/or whole lobes, that would be very helpful as well. In particular, the lobes would be helpful, as well as ROIs most relevant for AD (e.g. entorhinal cortex and temporal pole [Desikan et al., 2009]). Thanks, Dana > > >---------------------------------------------------------------------- > >Message: 1 >Date: Wed, 13 May 2009 08:54:59 -0400 (EDT) >From: rahul(a)nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] Literature values for cortical thickness >To: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> >Cc: freesurfer(a)nmr.mgh.harvard.edu, Falk L?sebrink > <falk.luese(a)gmx.net> >Message-ID: > <49194.70.23.239.45.1242219299.squirrel(a)mail.nmr.mgh.harvard.edu> >Content-Type: text/plain;charset=iso-8859-1 > >Hi Falk, > >We do indeed have cortical thickness values for each of the parcellation >units for a range of subjects (healthly elderly, middle age and young >controls and Alzheimer's disease subjects). Which parcellation units are >you looking for? A whole lobe? > >Best, > >rahul > > > Hi Falk, > > > > we published some values in our Cerebral Cortex paper , but I suspect the > > effective thickness will vary a bit as a function of pulse sequence, and > > certainly it will vary with things like age. Rahul has probably tabulated > > by parcellation unit if that helps. > > > > cheers > > Bruce > > > > On Wed, 13 May > > 2009, Falk Lüsebrink wrote: > > > >> Hi everyone, > >> > >> > >> > >> As I dont do a study in which I compare a group of subjects with some > >> kind > >> of abnormality with a control group I was looking for literature values > >> for > >> cortical thickness. The only paper I found which was written by von > >> Economo > >> et al. in 1925 doing a post-mortem analysis. > >> > >> > >> > >> Are there any more recent sources available which maybe even cover > >> in-vivo > >> values for regional cortical thickness? Actually Im looking for average > >> values across the whole lobes. > >> > >> > >> > >> Thanks in advance, > >> > >> Falk > >> > >> > > > >------------------------------ >

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RES: [Freesurfer] Re: Literature values for cortical thickness
by Pedro Paulo de Magalhaes Oliveira Junior 13 May '09

13 May '09

We have build a normative base with 68 subjects sampled from the average brazilian population. we are really interested in conducting / cooperating in a multicenter study. Enviado do meu celular Nokia -----Msg original----- De: Dana W. Moore Enviada: 13/05/2009 18:46:08 Para: freesurfer(a)nmr.mgh.harvard.edu Assunto: [Freesurfer] Re: Literature values for cortical thickness Actually, I have also been looking for cortical thickness normative values. We have run our first few research subjects with FreeSurfer (a normal control and several patients with neurodegenerative disorders), and I wanted to see if the thickness values we're getting are in the normal range. I have two papers: Salat et al. (2004) and Fischl & Dale (2000) in Cerebral Cortex. The Fischl and Dale gives average thickness for gyral and sulcal regions. Am I correct to guess that the average gyral and sulcal regions are taken by averaging the individual gyral and sulcal units from the aparc.a2005s.stats files? The Salat et al. article gives a global thickness measure--I was wondering how I would calculate this? Also, if thickness values are available for individual parcellation units and/or whole lobes, that would be very helpful as well. In particular, the lobes would be helpful, as well as ROIs most relevant for AD (e.g. entorhinal cortex and temporal pole [Desikan et al., 2009]). Thanks, Dana > > >---------------------------------------------------------------------- > >Message: 1 >Date: Wed, 13 May 2009 08:54:59 -0400 (EDT) >From: rahul(a)nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] Literature values for cortical thickness >To: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> >Cc: freesurfer(a)nmr.mgh.harvard.edu, Falk L?sebrink > <falk.luese(a)gmx.net> >Message-ID: > <49194.70.23.239.45.1242219299.squirrel(a)mail.nmr.mgh.harvard.edu> >Content-Type: text/plain;charset=iso-8859-1 > >Hi Falk, > >We do indeed have cortical thickness values for each of the parcellation >units for a range of subjects (healthly elderly, middle age and young >controls and Alzheimer's disease subjects). Which parcellation units are >you looking for? A whole lobe? > >Best, > >rahul > > > Hi Falk, > > > > we published some values in our Cerebral Cortex paper , but I suspect the > > effective thickness will vary a bit as a function of pulse sequence, and > > certainly it will vary with things like age. Rahul has probably tabulated > > by parcellation unit if that helps. > > > > cheers > > Bruce > > > > On Wed, 13 May > > 2009, Falk Lüsebrink wrote: > > > >> Hi everyone, > >> > >> > >> > >> As I dont do a study in which I compare a group of subjects with some > >> kind > >> of abnormality with a control group I was looking for literature values > >> for > >> cortical thickness. The only paper I found which was written by von > >> Economo > >> et al. in 1925 doing a post-mortem analysis. > >> > >> > >> > >> Are there any more recent sources available which maybe even cover > >> in-vivo > >> values for regional cortical thickness? Actually Im looking for average > >> values across the whole lobes. > >> > >> > >> > >> Thanks in advance, > >> > >> Falk > >> > >> > > > >------------------------------ > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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segmentation fault
by Kirk Gregory R. 13 May '09

13 May '09

Hi all, I got in the recon-all log #@# Cortical ribbon mask Tue May 12 17:56:52 CDT 2009 /home/gkirk/freesurfer/freesurfer/subjects/P21/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance P21 SUBJECTS_DIR is /home/gkirk/freesurfer/freesurfer/subjects Segmentation fault Linux debian01 2.6.26-1-amd64 #1 SMP Mon Dec 15 17:25:36 UTC 2008 x86_64 GNU/Linux recon-all exited with ERRORS at Tue May 12 18:10:33 CDT 2009 running build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0 Linux debian01 2.6.26-1-amd64 #1 SMP Mon Dec 15 17:25:36 UTC 2008 x86_64 GNU/Linux i have gotten 4 of these out of 21 ADNI data sets, I saw Nurunisa at Barry Kosofsky's site reported this also and Nick ask here to send the data set. 11 Nov 2008, got any info on this one ?, i am guessing it is a data quality issue that is breaking something in an uncontrolled way. thanks Greg.

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Freesurfer May 2009