Just to add to this.
The grey colour seems odd to me. The grey colour defaults when there are
no scalars to be read, if it was zero it would be a colour, VTK's default
lookup table is red. If you open the vtk file in a text editor and search
for the "SCALARS" and "VECTORS", these should contain real number.
Cheers,
Brian
> Hi,
>
> Not sure what you mean by a little odd.
> I don't think the warning is a problem, but you can check
> by running the tutorial data from the FSLCourse (see
> the main FSL web pages for links) and see if you get
> the same result for the vertex analysis there, as it only
> contains 8 subjects and does not survive FDR correction
> either. Also, if you are worried about your own images,
> then you should first view them in FSLView, and if that
> is OK then another quick check is just to look at the range
> with fslstats and the -R option, as that will normally pick
> out any problems in headers or intensities.
>
> All the best,
> Mark
>
>
> On 14 Sep 2009, at 03:18, Chien-Han Lai wrote:
>
>> Dear Mark:
>> I think the vectors of output file is a little odd (but color looks
>> appropriate).
>> Does the warning mean anything I should pay attention to?
>> Thank you
>> Dr. Lai
>>
>> --- 09/9/12 (六),Mark Jenkinson <[log in to unmask]> 寫道:
>>
>> 寄件者: Mark Jenkinson <[log in to unmask]>
>> 主旨: Re: [FSL] FIRST bug
>> 收件者: [log in to unmask]
>> 日期: 2009年9月12日,六,上午12:46
>>
>> Hi,
>>
>> Threshold of 0 in FDR means that nothing survived the correction,
>> so I'm not surprised about the lack of colours. However, the
>> warning is a bit odd. Does the output of the vertex analysis
>> look OK? That is, does it have colours and vectors in
>> appropriate places.
>>
>> All the best,
>> Mark
>>
>>
>>
>> On 11 Sep 2009, at 09:56, Chien-Han Lai wrote:
>>
>> > Dear FSL experts:
>> > Recently I tried FIRST function of FSL. When I perform FDR step
>> (surface_fdr step), I find the following messages in the terminal
>> window. Can anybody tells me what does that represent?
>> > open file sub_PA_L_Amyg1_pvals.vtk to save.
>> > succesfully opennded file sub_PA_L_Amyg1_pvals.vtk to save.
>> > FDR threshold is 0
>> > ** WARNING: posn not header size (0, 348)
>> > open file sub_PA_L_Amyg1_Fthresh.vtk to save.
>> > succesfully opennded file sub_PA_L_Amyg1_Fthresh.vtk to save.
>> >
>> > Besides, I view the Fthresh vtk file and there is wrong message too.
>> > The amygdala view is also just grey color (no other colors).
>> >
>> > Thank you for your kind help.
>> > Any comment will be very appreciated.
>> > Dr. Lai
>> >
>> >
>> > ___________________________________________________
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>>
>> ___________________________________________________
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>
>
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