Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

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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X11 problems
by Buchmann Andreas 13 May '09

13 May '09

Dear Freesurfer Experts, I recently installed freesurfer. In my first subject, it did the largest part of the calculations (recon-all all) but ended up with the following error: #@# Cortical ribbon mask Tue May 12 22:29:18 CEST 2009 /Applications/freesurfer/subjects/sleep001_RJ/mri \n mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance sleep001_RJ \n dyld: Library not loaded: /usr/X11/lib/libfontconfig.1.dylib Referenced from: /Applications/freesurfer/lib/vtk/lib/vtk-5.2/libvtkHybrid.5.2.dylib Reason: Incompatible library version: libvtkHybrid.5.2.dylib requires version 5.0.0 or later, but libfontconfig.1.dylib provides version 3.0.0 Trace/BPT trap Darwin hpsystem.kispi.int 9.2.2 Darwin Kernel Version 9.2.2: Tue Mar 4 21:17:34 PST 2008; root:xnu-1228.4.31~1/RELEASE_I386 i386 recon-all exited with ERRORS at Tue May 12 22:29:20 CEST 2009 How can I fix this incompatibility? Best regards Andreas Error log: SUBJECT sleep001_RJ DATE Tue May 12 22:29:20 CEST 2009 USER EGI HOST hpsystem.kispi.int PROCESSOR i386 OS Darwin Darwin hpsystem.kispi.int 9.2.2 Darwin Kernel Version 9.2.2: Tue Mar 4 21:17:34 PST 2008; root:xnu-1228.4.31~1/RELEASE_I386 i386 $Id: recon-all,v 1.133.2.42 2009/04/01 15:53:05 nicks Exp $ /Applications/freesurfer/bin/recon-all PWD /Applications/freesurfer/subjects/sleep001_RJ/mri CMD mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance sleep001_RJ ********************************************************************************************** IMPORTANT: The contents of this email and any attachments are confidential. They are intended for the named recipient(s) only. If you have received this email in error, please notify the system manager or the sender immediately and do not disclose the contents to anyone or make copies thereof. *** eSafe scanned this email for viruses, vandals, and malicious content. *** **********************************************************************************************

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Literature values for cortical thickness
by Falk Lüsebrink 13 May '09

13 May '09

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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aseg.volume.stats.dat problem
by anita di iasio 13 May '09

13 May '09

Hi all, version FreeSurfer 4.3.0 Problem: when I run qdec and I generate Stats Data, I can't import aseg.volume Command line shows this error: ERROR: QdecDataTable::Load could not find column named 'fsid' or 'ID' in /home/anita/freesurfer/subjects/qdec/stats_tables//aseg.volume.stats.dat! The facts is: the first line of aseg.volume.stats.dat is "Measure:volume Left-Cerebral-White-Matter Left-Cerebral-Cortex....." and happens the mentioned problem but if I change in "fsid Left-Cerebral-White-Matter Left-Cerebral-Cortex Left-Lateral-Ventricle Left-Inf-Lat-Vent...." I can import the aseg.volume and all go right. Is it a bug?Can you fix it? Thanks all, Anita di Iasio

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How to complete gracefully
by Martin Kavec 13 May '09

13 May '09

Hi, I have a bunch of analyzes (about 30), for which recon-all -all terminates prematurely at mris_volmask (and core is created). On one case I ran the mris_volmask and the rest of analysis by executing commands manually, which went fine, but it's laborious. Is there quicker way to complete the recon-all -all without need to go over the whole -autorecon3? ( for some reasons -make all starts the whole analysis over, which is not really necessary). Thanks in advance, Martin

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Fwd: Erro no FS
by Pedro Paulo de Magalhães Oliveira Junior 12 May '09

12 May '09

I have a researcher here who experienced a crash in Bert dataset, any hints? ---------- Forwarded message ---------- From: João Ricardo Sato <jrsatobr(a)gmail.com> Date: 2009/5/12 Subject: Re: Erro no FS To: Pedro Paulo de Magalhães Oliveira Junior <ppaulojr(a)gmail.com> Pedro Paulo, I had no idea why the application crashed in the bert dataset. Can you ask this in FreeSurfer List? Joao Sato 2009/5/12 Pedro Paulo de Magalhães Oliveira Junior <ppaulojr(a)gmail.com> Qual versao do FS? > ----------------------------------------------------------- > Pedro Paulo de M. Oliveira Junior > Diretor de Operações > Netfilter & SpeedComm Telecom > --- Novo Netfilter 3.0 www.netfilter.com.br > > > > 2009/5/12 João Ricardo Sato <jrsatobr(a)gmail.com> > > PP, >> >> vc sabe o q poderia ser esse erro? Aconteceu rodando o recon-all no bert. >> >> 0513: dt=0.000062, rms=0.428 (0.000%), neg=0, invalid=1511 >> 0514: dt=0.000031, rms=0.428 (-0.000%), neg=0, invalid=1511 >> setting smoothness coefficient to 1.00 >> blurring input image with Gaussian with sigma=2.000... >> 0000: dt=0.000, rms=0.433, neg=0, invalid=1511 >> 0515: dt=0.000000, rms=0.433 (0.000%), neg=0, invalid=1511 >> 0516: dt=0.100000, rms=0.433 (-0.069%), neg=0, invalid=1511 >> blurSegmentation fault >> ERROR: mri_ca_register with non-zero status >> Linux andLinux 2.6.22.18-co-0.7.3 #1 PREEMPT Wed Apr 16 18:50:10 UTC 2008 >> i686 GNU/Linux >> >> recon-all exited with ERRORS at Tue May 12 15:16:07 EDT 2009 >> >> >> Abs >> >> Jsato >> > > -- Jsato

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RA position at the Martinos Center
by raij＠nmr.mgh.harvard.edu 12 May '09

12 May '09

We are seeking an RA for a data analysis oriented position. Previous experience with FreeSurfer FS-FAST and MEG/EEG MNE analysis stream is highly valued. Ability to use MATLAB for mathematical modeling of fMRI and MEG/EEG data is required. For details, please see http://www.nmr.mgh.harvard.edu/martinos/opportunities/employment.php#rs0326… Tommi Raij raij(a)nmr.mgh.harvard.edu --- Tommi Raij, M.D., Ph.D. TMS Core Director MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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