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. >>>> >>> >>> >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
