Hi Again,
(apologies for the many posts): I should add that none of this happens (and everything works fine - no warning and small clusters which look reasonable) if I use version 5.3.
Thank you,
Nicola
On 7/22/2016 2:10 PM, Nicola Toschi wrote:
Hi,
thanks - I tried using "abs" as well as a higher threshold, however the large, whole-brain cluster (as well as the warning messages) still remains.
Do the warnings:
WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin WARNING: 251446 NaNs found in volume
give any clues?
The strange thing is that everything is fine (small clusters and no warning) when I use t-tests )i.e. just the first or second line of the F test).
Thanks a lot for your time,
Nicola
On 07/21/2016 11:53 PM, Douglas N Greve wrote:
Try using abs instead of pos. abs (absolute) is more appropriate since an F test is unsigned. Also, I would go with a threshold of 2 and not 1.3. I'm just now finding out that such a low threshold can cause a lot of false postives on real data.
On 07/21/2016 05:32 PM, Nicola Toschi wrote:
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 > >
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