Hi,

here it is (I also pasted the mri_glmfit line):

odir=${prefix}_${meas}_${h}_fwhm${s}_${surf} #name output directory

mri_glmfit --y ${h}.fwhm${s}.${list}.${meas}.mgh --X ${matrix} \
--C ${C1} \
--glmdir ${odir} --surf fsaverage ${h} ${surf}

/usr/local/freesurfer6dev/bin/mri_glmfit-sim --glmdir ${odir} --cache ${t} pos

Note: it is the same code i use for the t-tests, which appear to work fine.

The content of the file ${C1} is

1       -1      0       0       0       0
1       0      -1       0       0       0


Thanks in advance!

Nicola



On 7/21/2016 5:38 PM, Douglas N Greve wrote:
what is your mri_glmfit-sim command line?

On 07/20/2016 05:56 PM, Nicola Toschi wrote:

Hi List,

I am getting a couple of strange error when running a 3-group F-test.

WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
WARNING: 251446 NaNs found in volume
analysis/Ftest/cache.th20.pos.sig.cluster.mgh...

And as a result, I consistently get huge clusters:

# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ CWP
CWPLow    CWPHi   NVtxs    WghtVtx   Annot
     1          inf       0  63247.45    -38.8  -19.0   66.9 0.00010
0.00000  0.00020  98722         inf  precentral

However, this doesn't happen when running t-tests on the same data.
Still, I think my F-contrast is correct (see below).

Thanks in advance for any advice!

Nicola

PS:

my F-contrast looks like this:

1       -1      0       0       0       0
1       0      -1       0       0       0

and my design matrix looks like this:

0       0       1       1       179     110
0       0       1       1       193     103
0       0       1       1       176     108
0       0       1       1       198     94
0       1       0       1       186     87
0       1       0       1       217     83
.....

and my versions are

# $Id: mri_surfcluster.c,v 1.57 2014/03/06 17:02:46 greve Exp $
# $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $



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