Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

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

2 1

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

3 3

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.

2 1

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.

1 1

average 4d volume
by jake＠nmr.mgh.harvard.edu 11 May '09

11 May '09

Hi! I tried to use mri_xvolavg to average a 4d nii volume, but does it need me to list each 3d volume separately? Is there a command that I can use to produce an average of a 4d volume, in one 3d image? Thanks in advance!! Jake

2 1

Unable to Open GUI
by Andrew Jahn 11 May '09

11 May '09

Hi, We are operating x86_64 redhat linux on a server, and we recently installed FreeSurfer on the surfer to help with running multiple recon-all's. However, whenever I attempt to run tkmedit or tksurfer, I get the following error: [andrew@scan2 Anatomicals]$ tkmedit Focus_reg_009 brainmask.mgz GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not surrported by display: :1.0 Is this a problem specific to the VNC Viewer I am using (Chicken of the VNC on a Mac OS X), or some other compilation problem? Thanks! -Andrew

1 0

tkmedit multiple orientation view
by Krajcsi Attila 11 May '09

11 May '09

Hi All, Is it possible to start tkmedit with the multiple orientation view as default? Thank you, Attila

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