Confirmed. I had tried 0 to 1 and the -bin option without success, but I hadn't gone further. 1e-8 or even 1e-4 does indeed do the trick:
fslmaths sphereres.nii.gz -thr 0.0001 -bin sphereres2.nii.gz
Thanks, Mark.
-Adam
-----Original Message-----
From: Mark Jenkinson [mailto:[log in to unmask]]
Sent: Tuesday, May 17, 2011 5:31 PM
To: [log in to unmask]
Subject: Re: [FSL] using fslmaths to create an roi
Dear Adam,
If you look, the problem is that the display range is ridiculously small
(-4e-13 to +5e-13) and that's why the image looks so weird. If you
restore the display range to something sensible (0 to 1) then it will
look fine. If you need a binary image then run it through fslmaths
with a threshold of something like 1e-8.
All the best,
Mark
On 17 May 2011, at 22:19, Thomas, Adam (NIH/NIMH) [E] wrote:
> I'm experience the same problem that Lara is when using the 1mm MNI standard:
>
> fslmaths $FSLDIR/data/standard/MNI152_T1_1mm -mul 0 -add 1 -roi 50 1 50 1 50 1 0 1 point -odt float
> fslmaths point -kernel sphere 9 -fmean sphereres -odt float
>
> The second fslmaths command takes about 9 minutes to run and produces an output images reminiscence of early abstract impressionism:
>
> http://dl.dropbox.com/u/37868/Screen%20shot%202011-05-17%20at%205.15.57%20PM.png
>
> Any ideas on what's going on? Or is there an alternative FSL command to quickly generate a spherical ROI?
>
> Cheers,
> -Adam
>
>
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Lara Foland
> Sent: Wednesday, April 20, 2011 6:07 PM
> To: [log in to unmask]
> Subject: Re: [FSL] using fslmaths to create an roi
>
> Thanks for the reply, but I'm actually trying to create an ROI based on a point (not an activation map).
>
> Everything with the commands below works great, as long as the radius size is 10mm or under. But whenever I increase the radius size to, say, 15, the resulting roi is distorted.
>
> Has anyone else run into this problem?
>
> fslmaths $FSLDIR/data/standard/MNI152_T1_2mm -mul 0 -add 1 -roi 50 1 50 1 50 1 0 1 point -odt float
> fslmaths point -kernel sphere 9 -fmean sphereres -odt float
>
> Thanks,
> Lara
>
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