Hi,
This is just a display range issue.
Your images will have the cal_min and cal_max set inappropriately
so that fslview doesn't look nice. Just change the display range
settings in the Min/Max box at the top of fslview and it will look good.
None of this affects the values that are stored in your image.
If you want, you can get rid of the bad cal_min and cal_max values
by just running your image through fslmaths (i.e. fslmaths image image)
and that will fix it.
All the best,
Mark
On 11 Nov 2008, at 19:10, Laura deSouza wrote:
> Hi everyone,
>
> I'm using the fslvbm tools on my 35 subjects, and on the 2nd step
> (fslvbm_2_template), i keep encountering a strange problem:
>
> when I view the template_4D_GM in fslview, it looks blank--only by
> looking
> closely can you see anything. it looks normal, but as if a "brightness
> setting" is turned all the way down, so that at first glance it's just
> blank. when i view the template and other output images using
> slicesdir, it
> looks just fine, brightness and all.
>
> i checked some of the intermediate files in the struc folder, and
> they have
> the same problem, starting with the subxxx_struc_brain_mixeltype
> files, for
> every subject. subxxx_struc_brain and files generated before it are
> fine!
>
> Has anyone encountered this before? is there a setting i'm missing on
> fslview, or is this supposed to be normal? Viewing the template_GM
> on top of
> the standard space template looks fine as well, it's just the files
> mentioned above that look "dim" in fslview.
>
> Thanks very much,
> Laura
>
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