totally agree with Mark.
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From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Mark Jenkinson [[log in to unmask]]
Sent: Friday, August 09, 2013 3:03 AM
To: [log in to unmask]
Subject: Re: [FSL] Changing image dimensions (fslroi?)
Hi,
I've got no idea how you ended up with that original file as it is weird!
It contains both a non-binary brain (at the top) and a binary mask (at the bottom).
Try turning the colourscale to Red-Yellow in FSLView (viewing the original nodif_brain) to see this.
So if you use fslroi to extract the bottom half of the image then you get (correctly) a binarised brain mask as that is what is contained in the bottom half of the original image. If you use fslroi to extract the top half, then you get a non-binary image.
That is:
fslroi nodif_brain.nii brain0 0 128 0 128 0 64
fslroi nodif_brain.nii brain1 0 128 0 128 64 64
where brain0 is the bottom half (binary image) and brain1 is the top half (non-binary image).
This explains what is going on with fslroi, but not why you have such a weird image to start with.
All the best,
Mark
On 9 Aug 2013, at 07:54, Jochem Jansen <[log in to unmask]>
wrote:
> Dear Mark,
>
> Thanks for your assistance. I've uploaded the file.
>
> 1. the file is a binary 0/1 files (also in fslview intensities)
> 2. changing the range of view doesn't change this.
>
> Hope you can figure out the problem (and solution)!
>
> regards,
> Jochem
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