Hi again,
meanwhile I understand the GLM DOF is defined by the difference of inputs and classes (groups).
Inputs - Groups = DOF
So I need more inputs than groups, is that right? But that also means the g3v0.fsgd example (http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V) can't work with only three inputs, nor is it possible to compare two runs of only one subject (that would be g2v0.fsgd with only two inputs).
Please correct me if I'm wrong, but are the following combinations not the same somehow?
Design 1: 1 0 Contrast 1: 1 -1 1 0 0 1
Design 2: 1 0 0 Contrast 2: 0.5 0.5 -1 0 1 0 0 0 1
Since the DOF of the first design is 1, that could be a workaround for the second combination (with DOF = 0). But still, I can't imagine a possibility to compare only two inputs of the same or different subjects. Or am I totally off the track?
Any comments would be appreciated! Thanks again, Georg
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Georg Homola Gesendet: Freitag, 17. Juli 2009 03:01 An: 'Freesurfer Mailing List' Betreff: [Freesurfer] Three classes and GLM
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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