Dear Philipp,
If you load in your pvals vtk file, and not the F-stat one, then you can see the p-values by adjusting the scalar display range within the surface properties pop-up (the same one that the slider is in). That, together with making a clipping box in the 3D brain (see the FSLView docs), so that you only see certain slices in the background should generate a figure very similar to Fig 8b. We actually used a slightly different piece of software to produce this figure (hence the different colourmap, which is not available in FSLView) but you can get a very similar image out of FSLView.
All the best,
Mark
On 6 Jul 2011, at 16:02, philipp thomann wrote:
> Dear Mark,
>
> thanks for your quick reply. Maybe I was not clear enough: I already ran surface_fdr and loaded the corresponding *Fthresh.vtk file in FSLView (showing that most effects survive correction). Now I would like to "illustrate" the p-values (as in Fig. 8b of the Patenaude paper). Sorry, but I was not able to find any information on how to do this in the course, FSLView or FIRST documentation.
>
> Thanks again
>
> Philipp
>
>
>
> -------- Original-Nachricht --------
>> Datum: Wed, 6 Jul 2011 15:20:42 +0100
>> Von: Mark Jenkinson <[log in to unmask]>
>> An: [log in to unmask]
>> Betreff: Re: [FSL] FSL-FIRST vertex analysis: converting F into p-value
>
>> Dear Philipp,
>>
>> The 3D view in FSLView will do this.
>> You need to run surface_fdr to get corrected statistics and then
>> just follow the directions for display in the practical session from
>> the FSL course.
>>
>> All the best,
>> Mark
>>
>> On 6 Jul 2011, at 14:58, philipp thomann wrote:
>>
>>> Dear FSL experts,
>>>
>>> is there any FSLview driven way to show the color-coded p-values of a
>> given analysis (e.g. group comparison or correlation) or do you have to use
>> fslmaths for this purpose? If so, how? I'd like to illustrate my results as
>> shown in the Patenaude paper (Neuroimage 2011).
>>>
>>> Any advice is highly appreciated
>>>
>>> Philipp
>>>
>>>
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