Freesurfer May 2009

freesurfer@nmr.mgh.harvard.edu

81 participants
126 discussions

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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talairach transform fails in autorecon1
by ckeller＠nmr.mgh.harvard.edu 12 May '09

12 May '09

When trying to perform an auto recon on MRI_1.nii in /space/annecy/12/users/adykstra/cashlab/MRI/BW10/mri/, I get the following error during autorecon1: ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Tue May 12 10:34:18 EDT 2009 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue May 12 10:34:19 EDT 2009 /autofs/space/annecy_012/users/adykstra/cashlab/MRI/BW10_SURFER_OUTPUT/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux gate 2.6.9-78.0.5.ELsmp #1 SMP Wed Oct 8 07:12:03 EDT 2008 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Tue May 12 10:34:19 EDT 2009 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- So far I've identified and ruled out three possible reasons why this could be happening. 1. The localizer slice as the first slice in the volume. I removed that slice in the volume and tried again. 2. The field of view did not encompass the whole head in the anterior/posterior dimension, so I zero padded the edges - still didn't work. 3. The in-plane resolution of each slice is 512x512, which I learned from the help archive may be problematic. So, I tried both downsampling the volume and re-running autorecon1 as well as keeping the native resolution and giving autorecon1 the -cw256. This still didn't work. Please help. Thanks, Corey

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tcl scripts
by Krajcsi Attila 12 May '09

12 May '09

Hi All, In tksurfer is it possible to change the subject or the hemisphere from the tcl script we use? I couldn't find the solution for this on the tksurfer scripting wiki page. Maybe it's not possible. And is it possible to send parameters from the tksurfer command to the tcl script? Thank you, Attila

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Number of slices
by Al-Radaideh Ali 12 May '09

12 May '09

Dear FreeSurfer Experts, I noticed that the output images and even the 001.mgz in orig folder are re-sliced into 255 slices although my input was 160 slices. Is there any way I can get the output image with same number of slices? as I need to use the masks of some structure for further analysis. In other words, I have registered one image to the original MPRAGE I have used in freesurfer in order to get a cc mask and multiply it by the registered image and in this case I need the number of slices exactly the same. Any idea please? Thanks in advance Ali This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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postdoc position
by Elizabeth Mormino 11 May '09

11 May '09

Dear Freesurfer community: Postdoctoral positions are available in the Jagust Lab in the Helen Wills Neuroscience Institute at the University of California, Berkeley. We are studying brain aging using PET, structural MRI and fMRI. One project uses PET to measure brain beta-amyloid accumulation with the amyloid imaging agent PIB and relates these biochemical measurements to changes in brain structure and function. Another project uses PET measures of dopamine function and dopamine release with raclopride, and relates dopamine release to brain activation and working memory performance using fMRI. The goal of these projects is to understand how biochemistry affects frontal and medial temporal lobe working and episodic memory systems in aging. Please contact William Jagust: jagust(a)berkeley.edu for more information.

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Freesurfer May 2009