Hi FSLView has the following rules: if the image header contains
information about the best display range then it will use it. If that
isn't set, it estimates it from the data. I suspect that what's
happening is the the other viewers ignore that header information, and
the information being written into your header is not optimal for the
data. All of this should be independent of the actual data - though
of course you should also check that your data values do make sense.
Cheers.
On 14 Sep 2009, at 12:46, cliff wrote:
> oh! yes,it is just because of the contrast and brightness value.
> it seems both spm and MRIcro can adjust automatically, but fsl can't!
> after i set the value in fsl as the same in MRIcro, it become the
> same.
>
> does it mean that i don't need to care about these different when i
> try to do some analysis work on them?
> can i set up FSL also to adjust automatically?
>
> thanks!
>
> 2009/9/14 Mark Jenkinson <[log in to unmask]>
> Hi,
>
> I think that SPM may view the image in a different orientation to
> FSLView
> and also probably uses a different display range for the intensities.
> If your "grey" in FSLView is a uniform colour across the image with no
> features, then this probably indicates that the display range encoded
> in the image was inappropriate and you need to set the values for
> the display range (min and max) yourself in order to see the image
> clearly. Try this and see if that works.
>
> I doubt that any of this has any bearing on the use of fslmerge vs
> 3d to 4d. I think it is just about how images are typically
> displayed.
>
> All the best,
> Mark
>
>
>
> On 13 Sep 2009, at 10:24, cliff wrote:
>
> hello all,
> when i use "fslmerge" & "3d to 4d" tool in spm5 to merge a group
> of .hdr/.img file into a 4D file(.nii and .nii.gz) separately. i
> find that the image result showed in “fslview” is really different.
> then i find before merging into 4D file, just use “fslview” and
> spm5's “display” tool to check the same .hdr/.img file, the result
> is also different. the .hdr/img images showed in "fslview" are grey
> while showed in spm5 are more normal as we see usually.
>
> any body have these experience? can you tell me why?
>
> --
> Best regards!
>
> Sen-Hua Zhu
> Department of Psychology
> Sun Yat-sen University
> 135 Xingang West Road, Haizhu District, Guangzhou (510275), P.R.China
> 朱森华
> 中山大学心理学系
> 广东省广州市海珠区新港西路135号(510275)
>
>
>
>
> --
> Best regards!
>
> Sen-Hua Zhu
> Department of Psychology
> Sun Yat-sen University
> 135 Xingang West Road, Haizhu District, Guangzhou (510275), P.R.China
> 朱森华
> 中山大学心理学系
> 广东省广州市海珠区新港西路135号(510275)
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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