Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

Skull marrow and skull stripping
by Bo Shi 16 Aug '06

16 Aug '06

Howdy - It seems that the skullstripping step is having some trouble removing bone marrow (see attached image). Adjusting watershed values (I've tried as low as 5) does not make any significant improvement. Does anyone else have this issue? Can anyone provide any hints as to how I might get a better automated skull-strip? I've been manually removing the marrow but it's getting real old. Any thoughts would be much appreciated. Bo

3 9

subject failed autorecon1
by Chacko Cherian 15 Aug '06

15 Aug '06

Hi all, One of my subjects failed autorecon1 giving me this error: mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.646 0.464 -0.179 -16.319; -0.497 0.598 -0.245 -56.371; -0.008 0.303 0.757 179.232; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks mri_normalize: normalization failed Linux zoe 2.6.15-25-386 #1 PREEMPT Wed Jun 14 11:25:49 UTC 2006 i686 GNU/Linux recon-all exited with ERRORS at Tue Aug 15 16:21:26 MST 2006 Thanks in advance Chacko Cherian

2 1

tkmedit and tksurfer error
by Vishwadeep Ahluwalia 15 Aug '06

15 Aug '06

Hi Freesurfers, I just installed freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3 on FC5 linux,x86_64 platform. I'm getting the following errors for tkmedit and tksurfer respectively: tkmedit bert orig.mgz freeglut (tkmedit): Unable to create direct context rendering for window 'Medit: 'This may hurt performance. X Error of failed request: GLXBadContext Major opcode of failed request: 143 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 29 Current serial number in output stream: 29 tksurfer bert rh pial tksurfer: error while loading shared libraries: libtix8.1.8.4.so: wrong ELF class: ELFCLASS64 Please advise! regards, Vish PS: i'm using tksurfer-fc5 as given in the online instructions.

2 4

new .mat reader
by Doug Greve 14 Aug '06

14 Aug '06

Matlab .mat files (as produced by spm, for example) are going to be read into FreeSurfer differently starting tomorrow using code written by Thomas Nommer. The new version should be able to read in matlab5 and matlab4 matrices. This has been a problem with trying to read data produced by newer versions of spm. Tests indicate that there should be no difference between the new and old version, but let us know if you find something strange. This change only applies to the dev environment. doug -- 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

1 0

recon-all exited with errors
by Chacko Cherian 14 Aug '06

14 Aug '06

Hello all, One of the subjects I was running exited with ERRORS at the autorecon2 stage. This is how it exited. INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ $Id: mrisurf.c,v 1.441.2.1 2006/03/06 21:12:31 greve Exp $ before topology correction, eno=-62 (nv=111893, nf=223972, ne=335927, g=32) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 6825 ambiguous faces found in tessellation segmenting defects... defect 7 : 4 vertices have been added to the surface defect 21 : 13 vertices have been added to the surface defect 43 : 11 vertices have been added to the surface defect 44 : 3 vertices have been added to the surface defect 48 : 5 vertices have been added to the surface defect 53 : 9 vertices have been added to the surface total of 45 vertices has been added to the surface analyzing defects... mrisDefectAnalysis : defect 21 overlap defect 20 reading input surface /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/maketemp/norm/subj21/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Linux ernie 2.6.17.1 #4 PREEMPT Sat Aug 5 09:35:33 MST 2006 i686 pentium4 i386 GNU/Linux I have also attached the recon-all.log file for reference. Thanks in advance for your suggestions. Regards Chacko Cherian Arizona State University.

2 1

preprocessing error
by Cameron Ellis 14 Aug '06

14 Aug '06

Hi, While attempting to preprocess a subjects data I am given an error message (pasted below) as the motion correction step is implemented does anyone have an idea of what the libvnl_algo.so file is and where it may be located? I am not sure why it cannot be loaded. Thanks in advance for the help! Cameron ------- ************************** ----------- ------- Motion Correcting Run 006 ----------- ------- ************************** ----------- sess = SM2C2 Mon Aug 14 13:23:09 EDT 2006 mc-afni2 --i 006/f.bhdr --t 006/f.bhdr --frame 0 --o 006/fmc.bhdr --mcdat 006/fmc.mcdat /autofs/space/troy_001/users/FREESURFER/SM2C2_fsfast/func/SM2C2/bold mri_info --nframes --o /tmp/mriinfo.18814 006/f.bhdr mri_info: error while loading shared libraries: libvnl_algo.so: cannot open shared object file: No such file or directory ERROR: mc-sess failed

3 2

fsl
by Jiansong Xu 13 Aug '06

13 Aug '06

Dear Friends: My fsl was installed in the directory /usr/local/fsl. I can use fsl before download freesurfer, but I cannot open fsl any more after installed FreeSurfer. Any suggestions? Thanks Jiansong

2 1

surface coordinate
by Anqi Qiu 11 Aug '06

11 Aug '06

Hi, Can someone tell me how to transform the surface data back to have the same coordinates as the volume? Not centering it so I can superimpose the surface in the image volume. Thanks! Anqi Qiu Center for Imaging Science The Johns Hopkins University

1 0

error message at SkullLTA
by Chacko Cherian 11 Aug '06

11 Aug '06

Hello all, I got this error message while running one of my subjects. i checked the /mri directory but nu_noneck.mgz was not created instead nu.mgz was there. THanks in advance. Chacko Cherian. Arizona State University. reading labels out of gcam file... removing structures at least 25 mm from brain... 12620067 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 18 minutes and 46 seconds. #-------------------------------------- #@# SkullLTA Wed Aug 9 08:35:57 MST 2006 mri_em_register -skull -t transforms/talairach.lta nu_noneck. mgz /ud/chacko/freesurfer/average/RB_all_withskull_2006-02-15. gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacin g = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/ud/chacko/freesurfer/average/RB_all_withskull_2006-02-15.gca'... setting gca type = Normal gca type average std = 23.5 using min determinant for regularization= 55.2 0 singular and 6473 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... zcat: /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/maketemp/norm/subj21/mri/nu_noneck.mgz.gz: No such file or directory mghRead(/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/maketemp/norm/subj21/mri/nu_noneck.mgz, -1): read error mri_em_register: could not open input volume nu_noneck.mgz. Linux ernie 2.6.17.1 #4 PREEMPT Sat Aug 5 09:35:33 MST 2006 i686 pentium4 i386 GNU/Linux recon-all exited with ERRORS at Wed Aug 9 08:36:35 MST 2006

1 0

point correspondence of ?h.sphere.reg
by wanlin 11 Aug '06

11 Aug '06

Hello all: After processing cortex reconstruction using Freesurfer, i find that the number of vertices of ?h.sphere.reg for different people is different, How to make sure the point correspondence? the tutorial said that the ?h.sphere.reg file is the results of alignment between subjects and the standard template. If I want to perform hypothesis test for some features on every vertex, How should i do? thanks wanlin

3 2

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer