Hi John,
your second command may be incorrect. Try
> fslmaths point_mask -kernel sphere 10 -fmean sphere_mask
cheers
martin
John Herrington wrote:
> 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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