Matt,
flame is complaining because it cannot invert the f-contast matrix. This
is because you have the following t-contrasts:
1.000000e+00 -1.000000e+00
-1.000000e+00 1.000000e+00
1.000000e+00 0.000000e+00
0.000000e+00 1.000000e+00
and you're attempting to do an f-test which includes the first two
t-contrasts - and this gives a non-invertable f-contrast matrix [1 -1;
-1 1].
f-contrasts are not sensitive to the direction of the test (since they
test variances) and so you should not include [1 -1] and [-1 1] together
in an f-test. Instead, just have one or the other on its own (either one
will give the same result).
Best Regards, Mark.
On Thu, 30 Jun 2005, Matthew Hoptman wrote:
> 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
> MemShared: 0 kB
> Buffers: 421564 kB
> 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:/a!
fs!
> /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/af!
sw!
> 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/X!
11!
> 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:
>
--
Cheers, Mark.
Mark Woolrich.
Oxford University Centre for Functional MRI of the Brain (FMRIB),
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~woolrich
|