That should work. I just made a slightly different modification to the
code, which will be in 5.2
pmat = FTest(dof1, dof2, Fmat);
ind = find(rvarmat == 0); pmat(ind) = 1; % in case all time points
are same value
ind = find(pmat == 0); pmat(ind) = eps(0); % for REALLY sig voxels
fsigmat = -log10(pmat);
On 11/30/2012 11:25 AM, Caspar M. Schwiedrzik wrote:
> Hi Doug and Sebastian,
> thanks for your input. I think I can confirm that it is the problem
> that Sebastian described. FS 5.1 uses betainc, which returns 0, even
> in Matlab R2011b.
> The workaround that Sebastian suggested works, with a slight modification.
> In line 888 in fast_selxavg3.m currently reads
> ind = find(pmat == 0); pmat(ind) = 1;
> That seems wrong to me, as -log10(1) gives 1.
> I replaced line 888 with
> ind = find(pmat == 0); pmat(ind) = eps(0);
> -log10(eps(0)) gives 323.3062.
> Sebastian's solution of pmat(ind) = eps underestimates the
> significance because eps is by default eps(1).
> Does that make sense?
>
> I confirmed that the time courses indicate a highly significant
> difference; I have 27 runs of block design; the problem happens both
> for contrasts against baseline and for contrasts between conditions; I
> currently have this problem only in one subject.
>
> Thanks, Caspar
>
>
>
>
> 2012/11/29 Sebastian Moeller <sebastian.moell...@rwth-aachen.de>:
>> Hi Doug, hi Caspar,
>>
>> which matlab version are you using? We had some issues in the past that some
>> matlab 2007 and 2009 statistics toolbox versions returned p values of 0,
>> which obviously will not work as overlay, since those typically assume a
>> volume of:
>> -log10(p_value)
>> and on matlab 2007b (maci):
>>>> -log10(0.0)
>> ans =
>> Inf
>>>> -log10(eps)
>> ans =
>> 15.6536
>> So you should
>>
>> So test your input stat volumes for 0.0 and try to replace those with eps in
>> matlab and see how the overlay look then. Then try to teach fs-fast to do
>> this automagically :)
>> For saity checking have a look at the time course at those voxels (I assume
>> NHP block design data here), and remember if you can see the modulation in
>> the time courses with your bare eyes it will most likely be significant. So
>> at those voxels where the contrasts return zero I would expect really great
>> time courses with strong differences in modulation hiught between the
>> members of the -a and -c collections of contrast blocks.
>>
>> best
>> Sebastian
>>
>>
>> On Nov 29, 2012, at 09:55 , Douglas N Greve wrote:
>>
>>> Oh, I did not realize this was an fsfast issue, I thought you were using
>>> mri_glmfit. In that case, I'm not sure what could be causing the problem
>>> since the p-values are being computed by matlab. How many runs do you
>>> have? Is is a contrast that has a huge amount of power(eg, something vs
>>> fixation)? Does it happen in other subjects? One path to debugging is to
>>> run selxavg3-sess with -run-wise. This will create an analysis for each
>>> run separately. You can then see whether one run in particular is
>>> causing the problem.
>>> doug
>>>
>>> On 11/27/2012 08:34 PM, Caspar M. Schwiedrzik wrote:
>>>> Hi Doug,
>>>> I am afraid the p values are still too small in Free Surfer
>>>> Linux-centos4_x86_64-stable-pub-v5.1.0-full.
>>>> I redid
>>>> mkanalysis-sess
>>>> mkcontrast-sess
>>>> selxavg3-sess
>>>> in 5.1., it looks verz similar as in 4.5., including a whole of 0.0 in
>>>> the center of the cluster.
>>>> Any further advice?
>>>> Thanks,
>>>> Caspar
>>>>
>>>>
>>>>
>>>> 2012/11/26 Douglas Greve <gr...@nmr.mgh.harvard.edu>:
>>>>> No, it does not. With version 5 I went to a simple AR1 model instead.
>>>>> doug
>>>>>
>>>>>
>>>>>
>>>>> On 11/26/12 10:34 PM, Caspar M. Schwiedrzik wrote:
>>>>>> Hi Doug,
>>>>>> thanks for the input. What I meant is that in version 5.1,
>>>>>> mkanalysis-sess does not seem to recognize the -taumax flag to set the
>>>>>> maximum delay for the autocorrelation function.
>>>>>> Caspar
>>>>>>
>>>>>>
>>>>>> 2012/11/26 Douglas N Greve <gr...@nmr.mgh.harvard.edu>:
>>>>>>> On 11/26/2012 02:12 PM, Caspar M. Schwiedrzik wrote:
>>>>>>>> Hi Doug,
>>>>>>>> I'll do that.
>>>>>>>> Two quick follow-up questions regarding 5.1:
>>>>>>>> - it seems that I cannot specify taumax anymore in mkanalysis-sess. Is
>>>>>>>> there another argument that would allow me to set the autocorrelation?
>>>>>>> What do you mean by "set the autocorrelation"? You can turn it off with
>>>>>>> -no-whiten.
>>>>>>>
>>>>>>>> - in a block design, would refeventduration be the block length or the
>>>>>>>> length of the individual events within a block?
>>>>>>> The block length. This will not change the p-values, only percent signal
>>>>>>> change values (often not even looked at).
>>>>>>> doug
>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Caspar
>>>>>>>>
>>>>>>>> 2012/11/26 Douglas N Greve<gr...@nmr.mgh.harvard.edu>:
>>>>>>>>> Hi Caspar, I think I fixed this in later versions. If you upgrade, you
>>>>>>>>> can run the stats from 5.1 with recons from 4.5 (just don't mix recons
>>>>>>>>> from different versions).
>>>>>>>>> doug
>>>>>>>>>
>>>>>>>>> On 11/26/2012 01:15 PM, Caspar M. Schwiedrzik wrote:
>>>>>>>>>> Hi!
>>>>>>>>>> I ran into a funny problem when calculating contrasts in Freesurfer
>>>>>>>>>> 4.5.0.
>>>>>>>>>> Namely, the center of my cluster of significant voxels has a p-value
>>>>>>>>>> of -0.0, resulting in a funny whole where you would otherwise expect
>>>>>>>>>> to find the most significant voxel(s).
>>>>>>>>>> It seems that the p-value is too small. Is there a workaround
>>>>>>>>>> available?
>>>>>>>>>> Thank you very much,
>>>>>>>>>> Caspar
>>>>>>>>>> _______________________________________________
>>>>>>>>>> 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: 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
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>>>>>>>>> error
>>>>>>>>> but does not contain patient information, please contact the sender
>>>>>>>>> and
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>>>>>>>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>>>>>
>>> --
>>> 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: 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
>> --
>> Sebastian Moeller
>>
>> telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616
>> fax: 626-395-8826
>> German GSM: +49 - 15 77 - 1 90 31 41
>> mobile: +1-626-325-8598
>> +1-626-807-5242
>> US CDMA: +1-626-807-5242
>> moel...@caltech.edu
>>
>> Division of Biology
>> MC 114-96
>> California Institute of Technology
>> 1200 East California Boulevard
>> CA 91125, Pasadena
>> USA
>>
>
--
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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