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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