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/
>>>>>>>
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>>>>>>>
>>>>>>>
>>>>>>> The information in this e-mail is intended only for the person to whom
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>>>>>>> is
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>>>>> --
>>>>> 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/
>
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--
Sebastian Moeller
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