Hi Martin,
Thanks much for your input. Just tried the following, including your
revised second line:
fslmaths MNI152_T1_2mm_brain_mask -roi 50 1 50 1 50 1 0 1 point_mask
fslmaths point_mask -kernel sphere 10 -fmean sphere_mask
... and the final image (sphere_mask) is empty, as demonstrated on
visual inspection and using fslstats (like so):
> fslstats sphere_mask -R
0.000000 0.000000
Any ideas why?
Thank again - John
Martin M Monti wrote:
> 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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