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
>>>>>
>>>>>
>>>
>>
>
>
--
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
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.
