You should use fslmaths point_mask -kernel sphere 10 -fmean sphere_mask as
the sphere kernel only requires a radius in mm.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of John Herrington
Sent: Wednesday, February 27, 2008 10:45 AM
To: [log in to unmask]
Subject: Re: [FSL] fslroi -- spherical ROIs?
Hi,
I'm having trouble getting the syntax right to implement the strategy
written about below (a prior listserv email) for making a spherical ROI
mask. I've based the commands off of this email and the syntax output
of fslmaths. For example, I tried the following commands to make a
10x10x10mm sphere around point 50,50,50 in matrix space like so:
fslmaths MNI152_T1_2mm_brain_mask -roi 50 1 50 1 50 1 0 1 point_mask
fslmaths point_mask -kernel sphere 10x10x10 -fmean sphere_mask
The creation of the roi (the first command) works great, but not the
second command. I've tried a number of variations of the above syntax,
including putting everything into one fslmaths command, but all I get
for final output is either a single point ROI (i.e., the original
point_mask above) or a null image.
Could someone point me to the right command/syntax for implementing
this? I'm running it on Ubuntu Gutsy, FSL version 4.0.3-2.
Thanks - John
Mark Jenkinson wrote:
> Hi,
>
> It isn't possible to save an image that is not rectangular.
> But you can certainly mask an image by making everything zero outside a
> spherical region. The best way is to make a spherical mask and then
> just mask with this. To do that I recommend making an image with the
> everything zero except the centre voxel (you can easily do this with
> the -roi option in fslmaths) and then use the -kernel sphere option
> in fslmaths together with -fmean to turn this single voxel into a
> sphere. You can then (separately) use this result to mask your image
> in fslmaths.
>
> All the best,
> Mark
>
>
> On 18 Feb 2008, at 18:03, Martin M Monti wrote:
>
>> Hi, I know you can use fslroi to create cubic or similar ROIs -- using
>> it in its first form -- is there a way to produce a spherical ROI,
>> specifying the center in voxels/mm and a radius -- for example?
>>
>> cheers
>>
>> martin
>>
>
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