Hello everybody,
Since I was corresponding with a few persons separetly, it required resending
the same information to all of them.
So I am getting back to the general forum with my still unsolved problem.
To recap: when I run recaon-all pipeline as below:
[iwob...@huxley FMRI]$ recon-all -autorecon1 -i
NCVI-JR001TH_T1WIR_brain-conv.nii.gz
-subjid test -all -force
(with -autorecon1 option or without, similar situation occurs with -make option)
It fails to output many necessary files, including brainmask.mgz, and the error
message upon the completion of the pipeline is as follows:
ERROR: nu_correct
recon-all exited with ERRORS at Thu May 28 12:06:45 BST 2009
I attach a more detailed log file.
I hope that now somebody will be able to help me :)
Many thanks in advance,
Iwo
[iwob...@huxley FMRI]$ recon-all -autorecon1 -i
NCVI-JR001TH_T1WIR_brain-conv.nii.gz
-subjid test -all -force
INFO: /home/iwobohr/subjects/test exists with -i, but -force specified.
Deleting any previous source volumes
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0
INFO: SUBJECTS_DIR is /home/iwobohr/subjects
Actual FREESURFER_HOME /opt/freesurfer
-rw-rw-r-- 1 iwobohr iwobohr 99469 May 28 16:36
/home/iwobohr/subjects/test/scripts/
recon-all.log
Linux huxley 2.6.18-128.1.1.el5 #1 SMP Tue Feb 10 11:36:29 EST 2009 x86_64
x86_64 x8
6_64 GNU/Linux
nu_correct: Command not found.
/home/iwobohr/subjects/test
mri_convert /home/iwobohr/FMRI/NCVI-JR001TH_T1WIR_brain-conv.nii.gz
/home/iwobohr/s
ubjects/test/mri/orig/001.mgz
mri_convert /home/iwobohr/FMRI/NCVI-JR001TH_T1WIR_brain-conv.nii.gz
/home/iwobohr/su
bjects/test/mri/orig/001.mgz
$Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $
reading from /home/iwobohr/FMRI/NCVI-JR001TH_T1WIR_brain-conv.nii.gz...
TR=1000.00, 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 /home/iwobohr/subjects/test/mri/orig/001.mgz...
#--------------------------------------------
#...@# MotionCor Fri May 29 10:47:30 BST 2009
Found 1 runs
/home/iwobohr/subjects/test/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 /home/iwobohr/subjects/test/mri/orig/001.mgz
/home/iwobohr/subjects/test/mri/raw avg.mgz
/home/iwobohr/subjects/test
mri_convert /home/iwobohr/subjects/test/mri/rawavg.mgz
/home/iwobohr/subjects/test/ mri/orig.mgz --conform
mri_convert /home/iwobohr/subjects/test/mri/rawavg.mgz
/home/iwobohr/subjects/test/m ri/orig.mgz --conform
$Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $
reading from /home/iwobohr/subjects/test/mri/rawavg.mgz...
TR=1000.00, 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 (0.938, 0.9, 0.938) mm size and (256, 180, 256) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from 3 to 0 (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /home/iwobohr/subjects/test/mri/orig.mgz...
mri_add_xform_to_header -c
/home/iwobohr/subjects/test/mri/transforms/talairach.xfm
/home/iwobohr/subjects/test/mri/orig.mgz
/home/iwobohr/subjects/test/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#...@# Nu Intensity Correction Fri May 29 10:47:48 BST 2009
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2
/home/iwobohr/subjects/test/mri
/opt/freesurfer/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.7.2.1 2008/07/09 21:05:39 nicks Exp $
Linux huxley 2.6.18-128.1.1.el5 #1 SMP Tue Feb 10 11:36:29 EST 2009 x86_64
x86_64 x86_64 GNU/Linux
Fri May 29 10:47:48 BST 2009
nu_correct: Command not found.
tmpdir is ./tmp.mri_nu_correct.mni.30677
/home/iwobohr/subjects/test/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30677/nu0.mnc
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30677/nu0.mnc
$Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $
reading from orig.mgz...
TR=1000.00, 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.30677/nu0.mnc...
--------------------------------------------------------
Iteration 1 Fri May 29 10:47:54 BST 2009
nu_correct -clobber ./tmp.mri_nu_correct.mni.30677/nu0.mnc
./tmp.mri_nu_correct.mni.30677/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.30677/0/
nu_correct: Command not found.
ERROR: nu_correct
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