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 >>>>> >>>>> >
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