Hi Stephen,

yes, I even used the example data from the FSL course. For example, I use exactly the command suggested by the course for their data: "fslview template_GM -b .1,1 tmp_tfce_corrp_tstat1 -l Red-Yellow -b 0.8,1" When I look at fslview, then I can see highlighted "areas" and the min contrast/brightness ist 0.8 and the maximum is 1., as specified by the command I typed in. All the intensity ranges appear to be between 0 and 1. However, when I press the "reset contrast and brightness" button , then the minimum of the contrast/brightness becomes 0 and the maximum becomes 1.6373. The intensity however appears to stay between 0 and 1 (e.g. when I specify a voxel).

I would be very very grateful if anyone can explain to me what this means. I can't really imagine that I did something totally wrong because I used the course data and in order to get the tmp_fce_corrp_tstat1 file, I only had to fill in one command that is specified on the course website and I checked it over and over again but don't see anything wrong I might have done.

Many many thanks for any help! All best, Martina

2010/11/20 Stephen Smith <[log in to unmask]">[log in to unmask]>

Hi - are you sure you have the corrp image highlighted in the image overlay list (at the bottom of FSLView) when you are looking at (or resetting) the intensity display range? Indeed the 1-p values in this image should be in the range 0-1. You can also use fslstats to check the range of values in the corrp image.

Cheers.

On 19 Nov 2010, at 14:07, Martina Diamandis wrote:

Hi everyone,

I just stared using FSL and I strongly hope my question is not too stupid but I couldn't find the information somewhere else.

I did a VBM analysis using the standard script specified on the FSL homepage. When it comes to the point that I want to display my TFCE-based threholding results, I type in the basic command specified on the vbm homepage: fslview MNI152_T1_2mm fslvbm_tfce_corrp_tsts1 -l Red-Yellow -b 0.94

FSLview opens accordingly and I can't see any significant results. If I however press the "Reset contrast and brightness" button, the minimum value is 0, but the maximum value becomes 2.6992. And then I can see significant results.

Can someone explain to me how it is possible that the contrast maximum value becomes 2.6992? I thought that the contrast/brightness would show me the p-value? I also tried the same with the tutorial example vbm data and there, I can also see values higher than 1.

I'm very thankful to any explanation.

Many thanks, Martina

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Gwenaëlle Douaud, PhD

FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington OX3 9DU Oxford UK

Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717

www.fmrib.ox.ac.uk/~douaud

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