I'm having problems with recon-all. It used to work but recently, every
time I've used it, I get a nu_correct error. I don't think we have had
any freesurfer upgrades since the last time recon-all worked. Here's the
log. Anyone know what's wrong?
ip07:mperry[12] setenv SUBJECTS_DIR <path/to/subjects/dirs>
ip07:mperry[13] setenv FUNCTIONALS_DIR <path/to/subjects/dirs>
ip07:mperry[14] recon-all -stage1 -subjid subject_ID
########################################
program versions used
$Id: recon-all-nmr,v 1.50 2004/08/31 18:05:08 tosa Exp $
$Id: mri_motion_correct2,v 1.8 2004/10/04 22:52:12 greve Exp $
mri_convert --version
$
$Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v
6.12 2 003/11/14 16:52:24 stever Exp $
minctracc.c
$Header:
/software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v
96.5.2.1 2003/07/05 01:58:08 stever Exp $
$Header:
/software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v
6.12 2003/09/18 15:01:33 bert Exp $
$Header:
/software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6. 4
2001/04/24 13:38:42 neelin Exp $
$Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $
mri_convert --version
$
# $Id: mritotal.in,v 1.11.2.1 2003/11/17 06:01:15 stever Exp $
# $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $
$
$
$
$
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#######################################
INFO: SUBJECTS_DIR is <path/to/subjects/dirs>
---------------------------------------------
MotionCor Tue Mar 15 16:03:21 PST 2005
<path/to/subjects/dirs>/<subject_ID>/mri/orig
mri_motion_correct2 -o . -i 001 -i 002
tmpdir is ./tmp-mri_motion_correct2-23141
--------------------------------------------------------------
mri_motion_correct2 logfile is ./mri_motion_correct2.log
--------------------------------------------------------------
-----------------------------------------
Converting 001
Tue Mar 15 16:03:21 PST 2005
mri_convert 001
<path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_mo
tion_correct2-23141/cor-1.mnc
reading from 001...
TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00
i_ras = (-1, 0, 0)
j_ras = (0, -0, -1)
k_ras = (0, 1, -0)
writing to
<path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motion_
correct2-23141/cor-1.mnc...
-----------------------------------------
Converting 002
Tue Mar 15 16:03:29 PST 2005
mri_convert 002
<path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_mo
tion_correct2-23141/cor-2.mnc
reading from 002...
TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00
i_ras = (-1, 0, 0)
j_ras = (0, -0, -1)
k_ras = (0, 1, -0)
writing to
<path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motion_
correct2-23141/cor-2.mnc...
-----------------------------------------
Motion Correcting
<path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_
motion_correct2-23141/cor-2.mnc
Tue Mar 15 16:03:36 PST 2005
COG of v1: 2.191772 14.916920 -47.842663
COG of v2: 2.203371 14.932534 -47.776924
[trans] = 0.011599 0.015615 0.065739
Initial objective function val = 0.01807109
Final objective function value = 0.00892547
-----------------------------------------
Resampling
<path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motion_
correct2-23141/cor-2.mnc
Tue Mar 15 16:04:30 PST 2005
Transforming
slices:............................................................
................................................................................
................................................................................
....................................Done
-----------------------------------------
Averaging
Tue Mar 15 16:04:37 PST 2005
Processing:.....................................................................
................................................................................
................................................................................
...........................Done
-----------------------------------------
Converting Average to output
Tue Mar 15 16:04:41 PST 2005
mri_convert
<path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motion
_correct2-23141/avgvol.mnc . -tr 2730 -te 3.31 -TI 1000 -flip_angle
0.122173
reading from
<path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motio
n_correct2-23141/avgvol.mnc...
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)
Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
writing to ....
Started at: Tue Mar 15 16:03:21 PST 2005
Ended at: Tue Mar 15 16:04:46 PST 2005
mri_motion_correct2: done
---------------------------------------------
Nu Intensity Correction Tue Mar 15 16:04:46 PST 2005
mri_convert orig nu0.mnc
mri_convert orig nu0.mnc
reading from orig...
TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00
i_ras = (-1, 0, 0)
j_ras = (0, -0, -1)
k_ras = (0, 1, -0)
writing to nu0.mnc...
nu_correct -clobber nu0.mnc nu1.mnc
[mperry@ip07:<path/to/subjects/dirs>/<subject_ID>/mri/]
[2005-03-15 16:0 4:54] running:
/usr/pubsw/packages/mni/1.2/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 -d istance 200 -quiet -execute -clobber -nokeeptmp
-tmpdir /usr/tmp/nu_correct_2326 4/ nu0.mnc nu1.imp
spawn: exec of sharpen_volume failed: No such file or directory
nu_estimate_np_and_em: crashed while running sharpen_volume (termination
status= 65280)
nu_correct: crashed while running nu_estimate_np_and_em (termination
status=6528 0)
ERROR: nu_correct
------------------------------------------
Filesystem 1K-blocks Used Available Use% Mounted on
693727248 307742336 350745536 47% /space/aliens/1
------------------------------------------
recon-all exited with errors at Tue Mar 15 16:04:55 PST 2005