This is a bug in mri_glmfit in that it does not recognize that the dof is really 884 and not 0. The easiest thing to do right now is to explicitly compute the weighted combination, then do an osgm. You can use fscalc.fsl to do this.
doug
Georg Homola wrote:
Hi all,
I'm having some problems getting a second level fixed effects analysis started on my subjects. There are three runs (dofsum = 884) in each case I'd like to compare.
OSGM works fine so far, but when I apply a matrix like this:
1 0 0 0 1 0 0 0 1
To a contrast like that:
0.5 0.5 -1
mri_glmfit tells me: ERROR DOF = 0.
I also tried it with an FSGD file, so my approach was the same as for the Fsgdf3G0V example (http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V). That makes no difference.
When I divide the three runs into two classes, everything works fine again. But why the error with three classes?
Any ideas?
Thanks, Georg
$ mri_glmfit --surf 01 lh --y 01/gender.lh.cope1.sm05.mgz --yffxvar 01/gender.lh.varcope1.sm05.mgz --ffxdof 884 --glmdir 01/results/gender.sm05.lh --X xmat.mat --C test.mat --label $SUBJECTS_DIR/01/label/lh.cortex.label Reading source surface /data/freesurfer/01/surf/lh.white Number of vertices 149696 Number of faces 299388 Total area 96879.085938 AvgVtxArea 0.647172 AvgVtxDist 0.880017 StdVtxDist 0.256396
$Id: mri_glmfit.c,v 1.138.2.10 2009/05/18 15:41:44 greve Exp $ cwd /data/freesurfer/higher/highest/fixed cmdline mri_glmfit --surf 01 lh --y 01/gender.lh.cope1.sm05.mgz --yffxvar 01/gender.lh.varcope1.sm05.mgz --ffxdof 884 --glmdir 01/results/gender.sm05.lh --X xmat.mat --C test.mat --label /data/freesurfer/01/label/lh.cortex.label sysname Darwin FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /data/freesurfer/higher/highest/fixed/01/gender.lh.cope1.sm05.mgz logyflag 0 X xmat.mat usedti 0 labelmask /data/freesurfer/01/label/lh.cortex.label maskinv 0 glmdir 01/results/gender.sm05.lh IllCondOK 0 DoFFx 1 FFxDOF 884 yFFxVar /data/freesurfer/higher/highest/fixed/01/gender.lh.varcope1.sm05.mgz Creating output directory 01/results/gender.sm05.lh Loading y from /data/freesurfer/higher/highest/fixed/01/gender.lh.cope1.sm05.mgz Loading yffxvar from /data/freesurfer/higher/highest/fixed/01/gender.lh.varcope1.sm05.mgz Saving design matrix to 01/results/gender.sm05.lh/Xg.dat Matrix condition is 1 /data/freesurfer/01/label/lh.cortex.label /data/freesurfer/01/label/lh.cortex.label Found 141245 points in label. Pruning voxels by thr: 0.000000 Found 141245 voxels in mask Saving mask to 01/results/gender.sm05.lh/mask.mgh search space = 91409.8 DOF = 0 ERROR: DOF = 0
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