Hi
I emailed a little while ago about this, but I haven't heard any
solutions yet. As a check, I re-ran recon-all again this morning on a
local machine. Still crashing. Here is the output:
> recon-all -s $SUBJECT -motioncor
INFO: SUBJECTS_DIR is /autofs/space/megraid_043/seder/freesurfer
Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0_x86_64/dev
-rw-rw-r-- 1 dwakeman megclin 27336 Mar 10 18:01
/autofs/space/megraid_043/seder/freesurfer/nmr00069/scripts/recon-all.log
Linux rerun 2.6.9-22.0.2.106.unsupportedsmp #1 SMP Fri Jan 20 04:48:30
CST 2006 x86_64 x86_64 x86_64 GNU/Linux
#--------------------------------------------
[EMAIL PROTECTED] MotionCor Thu Mar 23 11:37:22 EST 2006
Found 2 runs
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz
#-----------------------------------------------
/autofs/space/megraid_043/seder/freesurfer/nmr00069
mri_motion_correct.fsl -o
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/rawavg.mgz -wild
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz
tmpdir is
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962
--------------------------------------------------------------
mri_motion_correct.fsl logfile is
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/rawavg.mgz.mri_motion_correct.fsl.log
--------------------------------------------------------------
-----------------------------------------
Converting
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz
Thu Mar 23 11:37:32 EST 2006
/autofs/space/megraid_043/seder/freesurfer/nmr00069
mri_convert
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img
-odt float
reading from
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz...
TR=2000.00, TE=3.25, TI=950.00, flip angle=7.00
i_ras = (-0, -1, -5.55112e-17)
j_ras = (-0.0401318, -0, -0.999194)
k_ras = (-0.999194, -0, 0.0401318)
changing data type from 4 to 3 (noscale = 0)...
writing to
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img...
Analyze Output Matrix
-0.000 -0.040 -0.999 91.684;
-1.000 -0.000 -0.000 129.675;
-0.000 -0.999 0.040 117.569;
0.000 0.000 0.000 1.000;
--------------------
INFO: set hdr.hist.orient to -1
-----------------------------------------
Converting
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz
Thu Mar 23 11:37:37 EST 2006
/autofs/space/megraid_043/seder/freesurfer/nmr00069
mri_convert
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img
-odt float
reading from
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz...
TR=2000.00, TE=3.25, TI=950.00, flip angle=7.00
i_ras = (-0, -1, -5.55112e-17)
j_ras = (-0.0401318, -0, -0.999194)
k_ras = (-0.999194, -0, 0.0401318)
changing data type from 4 to 3 (noscale = 0)...
writing to
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img...
Analyze Output Matrix
-0.000 -0.040 -0.999 91.684;
-1.000 -0.000 -0.000 129.675;
-0.000 -0.999 0.040 117.569;
0.000 0.000 0.000 1.000;
--------------------
INFO: set hdr.hist.orient to -1
-----------------------------------------
Motion Correcting
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img
Thu Mar 23 11:37:43 EST 2006
/autofs/space/megraid_043/seder/freesurfer/nmr00069
fsl_rigid_register -maxangle 90 -r
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img
-i
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img
-o
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.img
-tmpdir
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962
-cleanup
\n\n
$Id: fsl_rigid_register,v 1.14 2006/02/13 20:13:19 greve Exp $
Thu Mar 23 11:37:43 EST 2006
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.img
Reference is analyze, not converting
Input is analyze, not converting
Output is analyze, not converting
--------------------------------------
/autofs/space/megraid_043/seder/freesurfer/nmr00069
calling eval flirt -in
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.hdr
-out
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.hdr
-bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90
90 -interp trilinear -dof 6 -ref
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.hdr
-omat
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.fslmat
WARNING: Both reference and input images have an sform matrix set
The output image will use the sform from the reference image
Started at Thu Mar 23 11:37:43 EST 2006
Ended at Thu Mar 23 11:43:33 EST 2006
fsl_rigid_register Done
To check results, run:
tkmedit -f
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img
-aux
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.img
mv
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.img
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img
-----------------------------------------
Averaging
Thu Mar 23 11:43:33 EST 2006
/autofs/space/megraid_043/seder/freesurfer/nmr00069
inhibiting isotropic volume interpolation
1 of 2: reading
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img...
2 of 2: reading
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img...
INFO: analyzeRead(): min = 0, max = 1543
ERROR: premature end of file
ERROR: Success (0)
frame = 0, slice = 158, k=158, row = 0
nread = 0, nexpected = 256
fname =
height = 256
width = 256
depth = 160
nframe = 1
imnr0 = 1
imnr1 = 160
xnum = 256
ynum = 256
fov = 256.000000
thick = 1.000000
xstart = -128.000000
xend = 128.000000
ystart = -128.000000
yend = 128.000000
zstart = -80.000000
zend = 80.000000
type = 3
xsize = 1.000000
ysize = 1.000000
zsize = 1.000000
x ras = 0.000000 -1.000000 -0.000000
y ras = -0.040132 0.000000 -0.999194
z ras = -0.999194 0.000000 0.040132
c ras = 5.572693 0.674698 -8.076317
det(xyz_ras) = -1.000000
ras_good_flag = 1
brightness = 1
subject_name =
path_to_t1 =
fname_format =
analyzeRead2(): error reading from file
/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img
mri_average:
MRIread(/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img)
failed
Linux rerun 2.6.9-22.0.2.106.unsupportedsmp #1 SMP Fri Jan 20 04:48:30
CST 2006 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Thu Mar 23 11:43:38 EST 2006
--
Daniel Goldenholz
-----------------------------------------------------
Cell: 617-935-9421 http://people.bu.edu/danielg/
"Mavet v'chaim b'yad halashon"
"Life and death are in the hands of language"
- Proverbs 18:21
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