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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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi Doug,

do you think it will be possible for you to fix that bug in a week or so? It's somewhat crucial for my analysis.

Another thing I'd like to ask is: how feasible would it be to implement the --min operation into mri_concat? There is already a --max to compute the max of concatenated volumes, but I have to use fscalc.fsl to get the minimum of the inputs to calculate conjunctions (like Thomas Nichols recommended). So far so good. The problem I noticed is, since the surface has to be transformed into a volume and back, maybe due to some truncation effects the output surface is slightly different from the input (I don’t mean the operation itself) and won't match to a mask anymore. In other words: the signal looks the same, but masking will fail. There are two options to get around this: doing the masking with fscalc.fsl or apply a dummy operation to the mask with fscalc.fsl to "shift" the mask the same way as the signal and then do the masking with mri_mask. Therefore I ask because the calculations with mri_concat would be much faster and it seems slightly more accurate, too. What do you think?

Thanks again and sorry for the constant spamming... Georg

-----Ursprüngliche Nachricht----- Von: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Gesendet: Montag, 20. Juli 2009 21:10 An: Georg Homola Cc: 'Freesurfer Mailing List' Betreff: Re: [Freesurfer] Three classes and GLM / mri_glmfit dof bug

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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---

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