more errors - Freesurfer

25 Feb 2011


      Hi Bruce,
Thank you so much.
I got new error as follow
//////////////////////////////
Pom@pom-PC subjects]$ recon-all -s 211-1029-MKA_elan -all
Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux pom-PC.SME 2.6.35.6-45.fc14.i686 #1 SMP Mon Oct 18 23:56:17 UTC 2010
i686 i686 i386 GNU/Linux
nu_correct: Command not found.
#--------------------------------------------
#@# MotionCor Fri Feb 25 09:46:49 PST 2011
Found 1 runs
/usr/local/freesurfer/subjects/211-1029-MKA_elan/mri//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/211-1029-MKA_elan/mri//001.mgz
/usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/rawavg.mgz
/usr/local/freesurfer/subjects/211-1029-MKA_elan
mri_convert /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/rawavg.mgz
/usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz --conform
mri_convert /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/rawavg.mgz
/usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from
/usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/rawavg.mgz...
TR=4083.33, TE=14.00, TI=0.00, flip angle=90.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
Original Data has (1.0156, 1.0156, 3) mm size and (256, 256, 60) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz...
mri_add_xform_to_header -c
/usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/transforms/talairach.xfm
/usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz
/usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Nu Intensity Correction Fri Feb 25 09:47:00 PST 2011
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2
/usr/local/freesurfer/subjects/211-1029-MKA_elan/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 1.12 2009/12/16 20:15:41 greve Exp $
Linux pom-PC.SME 2.6.35.6-45.fc14.i686 #1 SMP Mon Oct 18 23:56:17 UTC 2010
i686 i686 i386 GNU/Linux
Fri Feb 25 09:47:00 PST 2011
nu_correct: Command not found.
tmpdir is ./tmp.mri_nu_correct.mni.17383
/usr/local/freesurfer/subjects/211-1029-MKA_elan/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17383/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17383/nu0.mnc -odt float
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from orig.mgz...
TR=4083.33, TE=14.00, TI=0.00, flip angle=90.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.17383/nu0.mnc...
--------------------------------------------------------
Iteration 1 Fri Feb 25 09:47:03 PST 2011
nu_correct -clobber ./tmp.mri_nu_correct.mni.17383/nu0.mnc
./tmp.mri_nu_correct.mni.17383/nu1.mnc -tmpdir
./tmp.mri_nu_correct.mni.17383/0/
nu_correct: Command not found.
ERROR: nu_correct
Linux pom-PC.SME 2.6.35.6-45.fc14.i686 #1 SMP Mon Oct 18 23:56:17 UTC 2010
i686 i686 i386 GNU/Linux
recon-all -s 211-1029-MKA_elan exited with ERRORS at Fri Feb 25 09:47:03 PST
2011
////////////////////////////////////////////
There is nu_correct in /usr/local/freesurfer/mni/bin as follows:
[Pom@pom-PC subjects]$ which nu_correct
/usr/local/freesurfer/mni/bin/nu_correct
thanks again.
-- 
Pom