It probably won't change it that much as it's just a t or F test.
doug
Georg Homola wrote:
Hi Doug,
so it should also be easily possible to compare only two runs of one subject as I initially wanted to do it. To compute the weighted combination would be a hell of a work for me, since I got almost 30 subjects with lots of copes and even more contrasts, so I would have to do that for more than a thousand variations manually (although partly scriptable).
I'd rather wait for the bugfix, if that's not going to take too long. Or is there an older version of mri_glmfit without that bug I could use only for the fixed effects part of my analysis?
A subsequent question for me is, how important is the exact number of dofs for mri_glmfit (or for the GLM in general) anyway? Since I got varying sums of dofs esp. because of motion outliers, I cumulated the dofs for every single case. The sums are in a range from 835 to 908. Now, could I just pass mri_glmfit (without that bug) the lowest number to stick with it, even though there are a bit more dofs in some cases, or would that change any results?
Thank you very much for your help in advance! Best regards, Georg
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Freitag, 17. Juli 2009 20:04 An: Georg Homola Cc: 'Freesurfer Mailing List' Betreff: Re: [Freesurfer] Three classes and GLM
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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