Hi,
My guess for the threshold may have been wrong.
If you just save out the results with no thresholding
or binarisation and then look at the values in FSLView
and play with the display range then you should be
able to work out what to do.
All the best,
Mark
On 8 Aug 2011, at 15:19, Andres Roman wrote:
> Tried it but again not working. Is it possible that something may still be
> wrong?
>
> --
> Andres Roman
>
>
>> From: Mark Jenkinson <[log in to unmask]>
>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>> Date: Fri, 5 Aug 2011 15:57:19 +0100
>> To: <[log in to unmask]>
>> Subject: Re: [FSL] ROI sphere problems
>>
>> Hi,
>>
>> This has been reported before.
>> It isn't a problem with the spherical convolution it is just very, very
>> tiny inaccuracies in the FFT implementation for larger spheres.
>> You only see the problem if you follow it with "-bin" in fslmaths.
>> If you instead follow it with "-thr 1e-10 -bin" then it should work fine.
>>
>> All the best,
>> Mark
>>
>>
>> On 5 Aug 2011, at 15:41, Andres Roman wrote:
>>
>>> Hi FSL crew,
>>>
>>> I am trying to create a ROI sphere in the DLPFC of 10mm but it seems to
>>> crash everytime I do it.
>>>
>>> I used the following comands to create a point first,
>>>
>>> fslmaths MNI152_T1_2mm_brain_mask -roi 128 1 162 1 100 1 0 1 mask -odt float
>>>
>>> This works perfect. But then when I try to expand this to a 10mm sphere I
>>> get a very weird result (which I attach as a pic from fslview). I used the
>>> following command to expand it:
>>>
>>> fslmaths mask.nii.gz -kernel sphere 10 -fmean -bin spheremask_10mm -odt
>>> float
>>>
>>> After this I used a smaller size of sphere (4mm) and it worked fine as you
>>> can see in the other pic I attach. I was wondering why this could happen.
>>> Thank you once more for your help.
>>>
>>> Best wishes
>>>
>>> --
>>> Andres Roman
>>> <10mm ROI sphere.gif>
>
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