Hi all,
When I try to run FSL for a higher level analysis with two groups and 5
EVs and 5 contrasts, I get the message:
MatrixType = Crout # Rows = 2; # Cols = 2
Trace: Crout(lubksb); GeneralSolvI; InvertedMatrix::Evaluate;
Gsmanager::f_ols_contrast; Gsmanager::ols_contrasts; Gsmanager::ols;
Gsmanager::run.
echo 13 > stats/dof
/bin/rm -f stats/zem* stats/zols* stats/mask*
Rendering using zmin=2.3 zmax=8
mkdir tsplot
/home/fsl/bin/tsplot . -f filtered_func_data -o tsplot
** ERROR: nifti_image_read(./stats/pe1): can't open header file
** ERROR: nifti_image_open(./stats/pe1): bad header info
Error: failed to open file ./stats/pe1
ERROR: Could not open image ./stats/pe1
Image Exception : #22 :: Failed to read volume ./stats/pe1
Finished FEAT at Thu Jun 30 08:39:17 EDT 2005
To view the FEAT report point your web browser at
/afs/cabi.rfmh.org/usr/hoptman/dv45/gng_grpdiff+.gfeat/cope2.feat/report.html
The FSLERRORREPORT follows:
Thanks for any suggestions,
Matt Hoptman
######################################################################
#### MACHINE INFORMATION
######################################################################
Uname:
Linux
df:
Filesystem 1K-blocks Used Available Use% Mounted on
AFS 9000000 0 9000000 0% /afs
quota:
Memory and Swap info:
total: used: free: shared: buffers: cached:
Mem: 4230225920 2579017728 1651208192 0 431681536 1672843264
Swap: 2154979328 0 2154979328
MemTotal: 4131080 kB
MemFree: 1612508 kB
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Cached: 1633636 kB
SwapCached: 0 kB
Active: 1504628 kB
Inactive: 550848 kB
HighTotal: 3276224 kB
HighFree: 1518376 kB
LowTotal: 854856 kB
LowFree: 94132 kB
SwapTotal: 2104472 kB
SwapFree: 2104472 kB
BigFree: 0 kB
######################################################################
#### ENVIRONMENT INFORMATION
######################################################################
FSLMULTIFILEQUIT=TRUE
FSLGNUPLOT=/home/fsl/bin/gnuplot
FSLMACHTYPE=i586-suse-linux-gcc3.3.1
FSLTCLSH=/home/fsl/bin/tclsh
FSLMACHINELIST=
FSLREMOTECALL=
FSLWISH=/home/fsl/bin/wish
FSLCONFDIR=/home/fsl/config
FSLBROWSER=/home/fsl/tcl/fslwebbrowser
FSLDISPLAY=/home/fsl/bin/display
FSLCONVERT=/home/fsl/bin/convert
FSLDIR=/home/fsl
FSLLOCKDIR=
FSLOUTPUTTYPE=NIFTI
FSL=/usr/local/fsl3.1/bin
MANPATH=/usr/local/man:/usr/local/man:/usr/local/man:/usr/local/dmp/man:/afs/cabi/usr/lim/lg/man:/usr/local/fsl3.1/man:/usr/share/man:/usr/local/man:/home/man:/usr/mni/man:/opt/pgsql/man:/opt/www/man:/home/SUREfit/man:/usr/X11R6/man:/opt/gnome/man:/usr/mdsplus/man:/usr/local/fsl/man:/usr/local/dmp/man:/usr/local/dmp/man:/usr/local/dmp/man
AFNI_PLUGINPATH=/home/abin
GNOME_PATH=:/opt/gnome:/usr
DCMDICTPATH=/usr/local/dmp/dcmtk341/lib/dicom.dic
LD_LIBRARY_PATH=/opt/pgsql/lib/:/usr/lib:/usr/X11R6/lib
XNLSPATH=/usr/X11R6/lib/X11/nls
PATH=/usr/local/dmp/bin:/afs/cabi/usr/lim/lg/bin:/usr/local/fsl3.1/bin:/usr/bin:/usr/local/AFNI:/afs/cabi/usr/lim/pythoncode:/local/pgsql/bin:/afs/cabi/usr/lim/bin.linux:/afs/cabi/usr/lim/ip/Linux/bin:/afs/cabi/usr/lim/ip/Linux/shells:/usr/afsws/bin:/usr/local/rsi/idl/bin:/afs/cabi/usr/lim/bin.neutral:.:/afs/cabi.rfmh.org/usr/hoptman/scripts:/afs/cabi.rfmh.org/usr/lim/ip/Linux/shells:/usr/pubsw/packages:/afs/cabi.rfmh.org/usr/lim/idl/faroi:/home:/home/hopt:/usr/mni/bin:/home/hopt/mni_reg/bin:/usr/vtk/bin:/opt/pgsql/bin:/opt/www/bin:/opt/php/bin:/home/SUREfit/bin:/home/fsl/bin:/usr/local/dmp/bin:/afs/cabi/usr/lim/lg/bin:/usr/local/fsl3.1/bin:/usr/bin:/usr/local/AFNI:/afs/cabi/usr/lim/pythoncode:/local/pgsql/bin:/afs/cabi/usr/lim/bin.linux:/afs/cabi/usr/lim/ip/Linux/bin:/afs/cabi/usr/lim/ip/Linux/shells:/usr/afsws/bin:/usr/local/rsi/idl/bin:/afs/cabi/usr/lim/bin.neutral:.:/afs/cabi.rfmh.org/usr/hoptman/scripts:/afs/cabi.rfmh.org/usr/lim/ip/Linux/shells:/usr/pubsw/packages:/afs!
/cabi.rfmh.org/usr/lim/idl/faroi:/home:/home/hopt:/usr/mni/bin:/home/hopt/mni_reg/bin:/usr/vtk/bin:/opt/pgsql/bin:/opt/www/bin:/opt/php/bin:/home/SUREfit/bin:/home/fsl/bin:/usr/local/dmp/bin:/afs/cabi/usr/lim/lg/bin:/usr/local/fsl3.1/bin:/usr/bin:/usr/local/AFNI:/afs/cabi/usr/lim/pythoncode:/local/pgsql/bin:/afs/cabi/usr/lim/bin.linux:/afs/cabi/usr/lim/ip/Linux/bin:/afs/cabi/usr/lim/ip/Linux/shells:/usr/afsws/bin:/usr/local/rsi/idl/bin:/afs/cabi/usr/lim/bin.neutral:.:/afs/cabi.rfmh.org/usr/hoptman/scripts:/afs/cabi.rfmh.org/usr/lim/ip/Linux/shells:/usr/pubsw/packages:/afs/cabi.rfmh.org/usr/lim/idl/faroi:/home:/home/hopt:/usr/mni/bin:/home/hopt/mni_reg/bin:/usr/vtk/bin:/opt/pgsql/bin:/opt/www/bin:/opt/php/bin:/home/SUREfit/bin:/home/fsl/bin:/usr/local/dmp/bin:/afs/cabi/usr/lim/lg/bin:/usr/local/fsl3.1/bin:/usr/bin:/usr/local/AFNI:/afs/cabi/usr/lim/pythoncode:/local/pgsql/bin:/afs/cabi/usr/lim/bin.linux:/afs/cabi/usr/lim/ip/Linux/bin:/afs/cabi/usr/lim/ip/Linux/shells:/usr/afsw!
s/bin:/usr/local/rsi/idl/bin:/afs/cabi/usr/lim/bin.neutral:.:/afs/cabi.rfmh.org/usr/hoptman/scripts:/afs/cabi.rfmh.org/usr/lim/ip/Linux/shells:/usr/pubsw/packages:/afs/cabi.rfmh.org/usr/lim/idl/faroi:/home:/home/hopt:/usr/mni/bin:/home/hopt/mni_reg/bin:/usr/vtk/bin:/opt/pgsql/bin:/opt/www/bin:/opt/php/bin:/home/SUREfit/bin:/home/fsl/bin:/usr/local/bin:/usr/bin:/usr/X11R6/bin:/bin:/usr/games:/opt/gnome/bin:/opt/kde3/bin:/usr/lib/java/jre/bin:/usr/mdsplus/bin:/usr/local/bin:/usr/afsws/bin:/usr/afsws/etc:/usr/local/dmp/bin:/usr/local/dmp/dcmtk341/bin:/usr/local/fsl/bin:/usr/local/AFNI:/usr/X11R6/bin:/bin:/opt/kde3/bin:/opt/kde2/bin:/usr/local/mni/bin:.:/usr/local/bin:/usr/afsws/bin:/usr/afsws/etc:/usr/local/dmp/bin:/usr/local/dmp/dcmtk341/bin:/usr/local/fsl/bin:/usr/local/AFNI:/usr/X11R6/bin:/bin:/opt/kde3/bin:/opt/kde2/bin:/usr/local/mni/bin:.:/usr/local/bin:/usr/afsws/bin:/usr/afsws/etc:/usr/local/dmp/bin:/usr/local/dmp/dcmtk341/bin:/usr/local/fsl/bin:/usr/local/AFNI:/usr/X11!
R6/bin:/bin:/opt/kde3/bin:/opt/kde2/bin:/usr/local/mni/bin:.:/usr/local/bin:/usr/afsws/bin:/usr/afsws/etc:/usr/local/dmp/bin:/usr/local/dmp/dcmtk341/bin:/usr/local/fsl/bin:/usr/local/AFNI:/usr/X11R6/bin:/bin:/opt/kde3/bin:/opt/kde2/bin:/usr/local/mni/bin:.
MODULEPATH=/usr/share/modules/versions:/usr/share/modules/modulefiles
MDSMSG_PATH=/usr/mdsplus/lib
MDS_PATH=/usr/mdsplus/tdi
IDL_PATH=+/afs/cabi/usr/lim/idl:+/usr/local/rsi/idl
PYTHONPATH=/afs/cabi/usr/lim/pythoncode
CLASSPATH=/home/fiswidgets-2.3/jars/fiswidgets-system.jar:/home/fiswidgets-2.3/jars/fiswidgets-all.jar:/home/fiswidgets-2.3/:/home/fiswidgets-2.3/jars/tools.jar:/home/fiswidgets-2.3/jars/afni.jar:/home/fiswidgets-2.3/jars/air.jar:/home/fiswidgets-2.3/jars/bvoyager.jar:/home/fiswidgets-2.3/jars/ifis.jar:/home/fiswidgets-2.3/pkg/ifis:/home/fiswidgets-2.3/jars/fiasco.jar:/home/fiswidgets-2.3/jars/fsl.jar:/home/fiswidgets-2.3/jars/nis.jar:/home/fiswidgets-2.3/jars/spiral.jar:/home/fiswidgets-2.3/jars/spm2.jar:/home/fiswidgets-2.3/jars/tal.jar
LGPATH=/afs/cabi/usr/lim/lg/bin
PKG_CONFIG_PATH=/opt/gnome/lib/pkgconfig
INFOPATH=/usr/local/info:/usr/share/info:/usr/info
ACLOCAL_PATH=/opt/gnome/share/aclocal
UIDPATH=/usr/mdsplus/uid/%U
MNI_DATAPATH=/usr/mni/data/N3
LD_LIBRARY_PATH=/opt/pgsql/lib/:/usr/lib:/usr/X11R6/lib
######################################################################
#### DIRECTORY INFORMATION
######################################################################
PWD:
/afs/cabi.rfmh.org/usr/hoptman/dv45/gng_grpdiff+.gfeat/cope2.feat
total 426
drwxr-xr-x 4 hoptman cabi 2048 2005-06-30 08:39 .
drwxr-xr-x 6 hoptman cabi 2048 2005-06-30 08:40 ..
-rw-r--r-- 1 hoptman cabi 233 2005-06-30 08:39 design.con
-rw-r--r-- 1 hoptman cabi 13403 2005-06-30 08:39 design_cov.gif
-rw-r--r-- 1 hoptman cabi 70965 2005-06-30 08:39 design_cov.ppm
-rw-r--r-- 1 hoptman cabi 14600 2005-06-30 08:39 design.fsf
-rw-r--r-- 1 hoptman cabi 68 2005-06-30 08:39 design.fts
-rw-r--r-- 1 hoptman cabi 50600 2005-06-30 08:39 design.gif
-rw-r--r-- 1 hoptman cabi 87 2005-06-30 08:39 design.grp
-rw-r--r-- 1 hoptman cabi 10 2005-06-30 08:39 design.lev
-rw-r--r-- 1 hoptman cabi 543 2005-06-30 08:39 design.mat
-rw-r--r-- 1 hoptman cabi 258918 2005-06-30 08:39 design.ppm
lrwxr-xr-x 1 hoptman cabi 15 2005-06-30 08:39 example_func.hdr
-> ../bg_image.hdr
lrwxr-xr-x 1 hoptman cabi 15 2005-06-30 08:39 example_func.img
-> ../bg_image.img
lrwxr-xr-x 1 hoptman cabi 12 2005-06-30 08:39
filtered_func_data.nii -> ../cope2.nii
-rw-r--r-- 1 hoptman cabi 7 2005-06-30 08:39 .fslcurrent
lrwxr-xr-x 1 hoptman cabi 11 2005-06-30 08:39 mask.nii ->
../mask.nii
-rw-r--r-- 1 hoptman cabi 558 2005-06-30 08:39 report.com
-rw-r--r-- 1 hoptman cabi 1588 2005-06-30 08:39 report.html
-rw-r--r-- 1 hoptman cabi 1364 2005-06-30 08:39 report.log
drwxr-xr-x 2 hoptman cabi 2048 2005-06-30 08:39 stats
drwxr-xr-x 2 hoptman cabi 2048 2005-06-30 08:39 tsplot
lrwxr-xr-x 1 hoptman cabi 15 2005-06-30 08:39
var_filtered_func_data.nii -> ../varcope2.nii
######################################################################
#### FEAT INFORMATION
######################################################################
Report log:
Started FEAT at Thu Jun 30 08:39:10 EDT 2005 on shannon
/bin/cp /afs/cabi.rfmh.org/usr/hoptman/dv45/gng_grpdiff+.gfeat/design.fsf
design.fsf
/home/fsl/bin/feat_model design
/home/fsl/bin/flame --cope=filtered_func_data --vc=var_filtered_func_data
--mask=mask --ld=stats --dm=design.mat --cs=design.grp --tc=design.con
--fc=design.fts --ols --nj=10000 --bi=500 --se=1 --fm --zlt=2.25 --zut=2.65
Log directory is: stats
Setting up:
nevs=2
ntpts=15
ngs=1
nvoxels=173563
Running:
An exception has been thrown
Runtime error:- detected by Newmat: matrix is singular
MatrixType = Crout # Rows = 2; # Cols = 2
Trace: Crout(lubksb); GeneralSolvI; InvertedMatrix::Evaluate;
Gsmanager::f_ols_contrast; Gsmanager::ols_contrasts; Gsmanager::ols;
Gsmanager::run.
echo 13 > stats/dof
/bin/rm -f stats/zem* stats/zols* stats/mask*
Rendering using zmin=2.3 zmax=8
mkdir tsplot
/home/fsl/bin/tsplot . -f filtered_func_data -o tsplot
** ERROR: nifti_image_read(./stats/pe1): can't open header file
** ERROR: nifti_image_open(./stats/pe1): bad header info
Error: failed to open file ./stats/pe1
ERROR: Could not open image ./stats/pe1
Image Exception : #22 :: Failed to read volume ./stats/pe1
Finished FEAT at Thu Jun 30 08:39:17 EDT 2005
To view the FEAT report point your web browser at
/afs/cabi.rfmh.org/usr/hoptman/dv45/gng_grpdiff+.gfeat/cope2.feat/report.html
######################################################################
Design Matrix:
%! VEST-Waveform File
/NumWaves 2
/NumPoints 15
/Skip 0
/Custom 0 design
/Custom 0 design
/PPheights 1.000000e+00 1.000000e+00
/Matrix
0.000000e+00 1.000000e+00
0.000000e+00 1.000000e+00
1.000000e+00 0.000000e+00
0.000000e+00 1.000000e+00
1.000000e+00 0.000000e+00
0.000000e+00 1.000000e+00
1.000000e+00 0.000000e+00
0.000000e+00 1.000000e+00
1.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00
0.000000e+00 1.000000e+00
0.000000e+00 1.000000e+00
1.000000e+00 0.000000e+00
######################################################################
Group Design Matrix:
%! VEST-Waveform File
/NumWaves 1
/NumPoints 15
/Matrix
2
2
1
2
1
2
1
2
1
1
1
1
2
2
1
######################################################################
Contrast Matrix:
%! VEST-Waveform File
/NumWaves 2
/NumContrasts 4
/PPheights 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
/Matrix
1.000000e+00 -1.000000e+00
-1.000000e+00 1.000000e+00
1.000000e+00 0.000000e+00
0.000000e+00 1.000000e+00
######################################################################
FTS Matrix:
%! VEST-Waveform File
/NumWaves 4
/NumContrasts 1
/Matrix
1 1 0 0
######################################################################
#### Main directory:
total 426
drwxr-xr-x 4 hoptman cabi 2048 2005-06-30 08:39 .
drwxr-xr-x 6 hoptman cabi 2048 2005-06-30 08:40 ..
-rw-r--r-- 1 hoptman cabi 233 2005-06-30 08:39 design.con
-rw-r--r-- 1 hoptman cabi 13403 2005-06-30 08:39 design_cov.gif
-rw-r--r-- 1 hoptman cabi 70965 2005-06-30 08:39 design_cov.ppm
-rw-r--r-- 1 hoptman cabi 14600 2005-06-30 08:39 design.fsf
-rw-r--r-- 1 hoptman cabi 68 2005-06-30 08:39 design.fts
-rw-r--r-- 1 hoptman cabi 50600 2005-06-30 08:39 design.gif
-rw-r--r-- 1 hoptman cabi 87 2005-06-30 08:39 design.grp
-rw-r--r-- 1 hoptman cabi 10 2005-06-30 08:39 design.lev
-rw-r--r-- 1 hoptman cabi 543 2005-06-30 08:39 design.mat
-rw-r--r-- 1 hoptman cabi 258918 2005-06-30 08:39 design.ppm
lrwxr-xr-x 1 hoptman cabi 15 2005-06-30 08:39 example_func.hdr
-> ../bg_image.hdr
lrwxr-xr-x 1 hoptman cabi 15 2005-06-30 08:39 example_func.img
-> ../bg_image.img
lrwxr-xr-x 1 hoptman cabi 12 2005-06-30 08:39
filtered_func_data.nii -> ../cope2.nii
-rw-r--r-- 1 hoptman cabi 7 2005-06-30 08:39 .fslcurrent
lrwxr-xr-x 1 hoptman cabi 11 2005-06-30 08:39 mask.nii ->
../mask.nii
-rw-r--r-- 1 hoptman cabi 558 2005-06-30 08:39 report.com
-rw-r--r-- 1 hoptman cabi 1588 2005-06-30 08:39 report.html
-rw-r--r-- 1 hoptman cabi 1364 2005-06-30 08:39 report.log
drwxr-xr-x 2 hoptman cabi 2048 2005-06-30 08:39 stats
drwxr-xr-x 2 hoptman cabi 2048 2005-06-30 08:39 tsplot
lrwxr-xr-x 1 hoptman cabi 15 2005-06-30 08:39
var_filtered_func_data.nii -> ../varcope2.nii
######################################################################
#### Stats directory:
total 6
drwxr-xr-x 2 hoptman cabi 2048 2005-06-30 08:39 .
drwxr-xr-x 4 hoptman cabi 2048 2005-06-30 08:39 ..
-rw-r--r-- 1 hoptman cabi 3 2005-06-30 08:39 dof
-rw-r--r-- 1 hoptman cabi 269 2005-06-30 08:39 logfile
######################################################################
#### Reg directory:
|
