Hi,
thanks for your reply. The mri_glmfit-sim was pasted below, here it is the dereferenced version:
/usr/local/freesurfer6dev/bin/mri_glmfit-sim --glmdir design_3groups_AgeGenderIq_area_lh_fwhm0_pial --cache 1.3 pos
thanks again,
Nicola
On 7/21/2016 11:13 PM, Douglas N Greve wrote:
That is the mri_glmfit command, I need the mri_glmfit-sim. Also, please do not include variables, just the full command with all dereferenced args
On 07/21/2016 03:28 PM, Nicola Toschi wrote:
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 $
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer