On 6/25/06, Sebastian Moeller <sebastian.moeller@lur.rwth-aachen.de > wrote:

Hi Anil,

On 26. Jun 2006, at 00:08 Uhr, freesurfer-request@nmr.mgh.harvard.edu
wrote:

> Message: 8
> Date: Sun, 25 Jun 2006 17:07:36 -0500
> From: "Anil Roy" <aroy85@gmail.com>
> Subject: Re: [Freesurfer] recon-all error
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
>       <627ebe090606251507s57777571wbd816d66196fc4f5@mail.gmail.com >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Skipped content of type multipart/alternative-------------- next part
> --------------
> INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> ERROR: /usr/local/freesurfer/subjects/F200 exists, delete or re-run
> with -force
> [root@dhcp-129-105-146-220 freesurfer]# recon-all -force -i
> /root/Desktop/F200.mnc -subjid F200 -sd /usr/local/freesurfer/subjects
> -all
> INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> INFO: /usr/local/freesurfer/subjects/F200 exists with -i, but -force
> specified.
> Deleting any previous source volumes
> Actual FREESURFER_HOME /usr/local/freesurfer
> -rw-rw-r--  1 root root 9126 Jun 25 15:42
> /usr/local/freesurfer/subjects/F200/scripts/recon-all.log
> Linux dhcp-129-105-146-220.speech.northwestern.edu
> 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386
> GNU/Linux
> WM removal version
> /usr/local/freesurfer/subjects/F200
>
>  mri_convert /root/Desktop/F200.mnc
> /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz
>
> mri_convert /root/Desktop/F200.mnc
> /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz
> reading from /root/Desktop/F200.mnc...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (1, 0, 0)
> j_ras = (0, 1, 0)
> k_ras = (0, 0, 1)
> writing to /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz...
> #--------------------------------------------
> #@# MotionCor Sun Jun 25 15:42:47 CDT 2006
> Found 1 runs
> /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz
> WARNING: only one run found. This is OK, but motion
> correction cannot be performed on one run, so I'll
> copy the run to rawavg and continue.
>
>  cp /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz
> /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz
>
> /usr/local/freesurfer/subjects/F200
>
>  mri_convert /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz
> /usr/local/freesurfer/subjects/F200/mri/orig.mgz --conform
>
> mri_convert /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz
> /usr/local/freesurfer/subjects/F200/mri/orig.mgz --conform
> reading from /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (1, 0, 0)
> j_ras = (0, 1, 0)
> k_ras = (0, 0, 1)
> Original Data has (1, 1, 1) mm size and (181, 217, 181) voxels.
> Data is conformed to 1 mm size and 256 voxels for all directions
> changing data type from 4 to 0 (noscale = 0)...
> MRIchangeType: Building histogram
> Reslicing using trilinear interpolation
> writing to /usr/local/freesurfer/subjects/F200/mri/orig.mgz...
>
>  mri_add_xform_to_header -c
> /usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm
> /usr/local/freesurfer/subjects/F200/mri/orig.mgz
> /usr/local/freesurfer/subjects/F200/mri/orig.mgz
>
> INFO: extension is mgz
> #--------------------------------------------
> #@# Nu Intensity Correction Sun Jun 25 15:43:04 CDT 2006
>
>  mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2
>
> /usr/local/freesurfer/subjects/F200/mri
> /usr/local/freesurfer/bin//mri_nu_correct.mni
> --i orig.mgz --o nu.mgz --n 2
> nIters 2
> $Id: mri_nu_correct.mni,v 1.3 2005/12/08 01:27:21 greve Exp $
> Linux dhcp-129-105-146-220.speech.northwestern.edu
> 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386
> GNU/Linux
> Sun Jun 25 15:43:04 CDT 2006
> Program nu_correct, built from:
> Package MNI N3, version 1.10, compiled by nicks@kani
> (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27
> tmpdir is ./tmp.mri_nu_correct.mni.3620
> /usr/local/freesurfer/subjects/F200/mri
> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3620/nu0.mnc
> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3620/nu0.mnc
> Can't find the talairach xform
> '/usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm'
> Transform is not loaded into mri
> reading from orig.mgz...
>   Talairach transform
> /usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm does
> not exist ...
> Cannot load tal xfm file
> /usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (0, 1, 0)
> writing to ./tmp.mri_nu_correct.mni.3620/nu0.mnc...
>
> --------------------------------------------------------
> Iteration 1 Sun Jun 25 15:43:10 CDT 2006
> nu_correct -clobber ./tmp.mri_nu_correct.mni.3620/nu0.mnc
> ./tmp.mri_nu_correct.mni.3620/nu1.mnc
> [root@dhcp-129-105-146-220.speech.northwestern.edu:/usr/local/
> freesurfer/subjects/F200/mri/] [2006-06-25 15:43:11] running:
>   /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log
> -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask
> -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber
> -nokeeptmp -tmpdir /usr/tmp/nu_correct_3670/
> ./tmp.mri_nu_correct.mni.3620/nu0.mnc
> ./tmp.mri_nu_correct.mni.3620/nu1.imp
>
> /usr/local/freesurfer/mni/bin/volume_stats: error while loading shared
> libraries: libstdc++.so.5: cannot open shared object file: No such
> file or directory

        Here is the part where it breaks; the freesurfer program you use most
likely was compiled with gcc 3.x.x, while FC4 is using gcc 4.x.x. The
result from the switch in compilers is that you only have a
libstdc++.so.6. If you install the following rpm from your installation
medium (or any source from the internet)
compat-libstdc++-33-3.2.3-47.fc4.i386; it should work. One caveat, I
never used FC4, so I might be way off.

Ahoi & good luck
        Sebastian

> nu_estimate_np_and_em: crashed while running volume_stats (termination
> status=32512)
> nu_correct: crashed while running nu_estimate_np_and_em (termination
> status=32512)
> ERROR: nu_correct
> Linux dhcp-129-105-146-220.speech.northwestern.edu
> 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386
> GNU/Linux
>
> recon-all exited with ERRORS at Sun Jun 25 15:43:11 CDT 2006
>
--
Sebastian Moeller

Tel.: 04 21 - 2 18 - 78 38 oder 96 91
Fax.: 04 21 - 2 18 - 90 04
GSM:  01 62 - 3 25 45 59
moeller@brain.uni-bremen.de

AG Kreiter / FB 2
Institut fuer Hirnforschung III
Abteilung Theoretische Neurobiologie
Universitaet Bremen
Biogarten
Hochschulring 16a
Postfach 33 04 40
28359 Bremen