Freesurfer August 2006

freesurfer@nmr.mgh.harvard.edu

48 participants
74 discussions

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.

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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

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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

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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

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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

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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

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what standard are the coordinates from %surfer command line?
by Nguyen, Thang Q 11 Aug '06

11 Aug '06

Hello all, For some reason, when I load a specific analysis surface, the vertex and cursor position freezes on the GUI. Is there any way of determining it from the %surfer command line, i.e. a translation of some sort? % surfer: dmin=0.2796, vno=31207, x=-32.1396, y=-9.1446, z=-16.7376 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 31207 marked (curv=0.000000, stat=0.000000) x = (-32.1, -9.1, -16.7), n = (-0.8, 0.2, 0.5). % Unmarking 13794 surfer: vertex 13794 unmarked Thank you for your time, -Thang

1 0

no brain.tri and brain.mgz
by Jiansong Xu 10 Aug '06

10 Aug '06

Dear Friends: I'm playing with the tutorial. I didn't get the brain.tri and brain.mgz files after the first step, see below for the command: recon-all -subjid bert -autorecon1 Best Jiansong

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single button mouse
by Jiansong Xu 10 Aug '06

10 Aug '06

Dear Friend: I'm using Mac OSX with single button mouse. How can I deal with "right click", "middle click", and "left click" Thanks Jiansong

2 1

Copying control points file?
by Jake Freimer 10 Aug '06

10 Aug '06

If I have the same subject on 2 different computers, but I edited the control points on one, can I just copy the tmp/control.dat file over to the other computer and rerun autorecon2-cp, or are there other files it refrences? Thanks -- -Jake

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Freesurfer August 2006