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 $
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
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
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
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
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
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
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 > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
what version does it fail on? If a dev version, when did you download it?
On 07/22/2016 12:15 PM, Nicola Toschi wrote:
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 >> >>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi,
it's a dev version downloaded on Jan 17th 2016.
As mentioned in my other mail, I have uploaded a full glmdir at
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=akbem4mthlv
thanks for your time,
Nicola
On 7/22/2016 6:35 PM, Douglas N Greve wrote:
what version does it fail on? If a dev version, when did you download it?
On 07/22/2016 12:15 PM, Nicola Toschi wrote:
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 >>> >>>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
That version may have had a bug. Try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit btw, you should not be using the dev version of recon-all
On 07/22/2016 02:01 PM, Nicola Toschi wrote:
Hi,
it's a dev version downloaded on Jan 17th 2016.
As mentioned in my other mail, I have uploaded a full glmdir at
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=akbem4mthlv
thanks for your time,
Nicola
On 7/22/2016 6:35 PM, Douglas N Greve wrote:
what version does it fail on? If a dev version, when did you download it?
On 07/22/2016 12:15 PM, Nicola Toschi wrote:
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 >>>> >>>>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Doug,
thank you - using this new version changed everything back to "normal" (small clusters, few results), so it may indeed have been a problem with that particular version.
Thanks again,
Nicola
On 7/22/2016 8:22 PM, Douglas N Greve wrote:
That version may have had a bug. Try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit btw, you should not be using the dev version of recon-all
On 07/22/2016 02:01 PM, Nicola Toschi wrote:
Hi,
it's a dev version downloaded on Jan 17th 2016.
As mentioned in my other mail, I have uploaded a full glmdir at
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=akbem4mthlv
thanks for your time,
Nicola
On 7/22/2016 6:35 PM, Douglas N Greve wrote:
what version does it fail on? If a dev version, when did you download it?
On 07/22/2016 12:15 PM, Nicola Toschi wrote:
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 >>>>> >>>>> >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Can you tar up the glmdir and send it to me on our filedrop? The first warning is not a problem. Not sure about the 2nd. doug
On 07/22/2016 08:10 AM, 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 > >
Hi,
I have uploaded it and the link should be
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=akbem4mthlv
Thanks!
Nicola
On 7/22/2016 6:31 PM, Douglas N Greve wrote:
Can you tar up the glmdir and send it to me on our filedrop? The first warning is not a problem. Not sure about the 2nd. doug
On 07/22/2016 08:10 AM, 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 >> >>
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Nicola Toschi