Hi,
Problem is that the input image is integer and so it tries to write
an output image that is integer too, but rounds down values to zero.
Try adding -odt float at the end of your fslmaths commands.
That should make it work for the MNI152_T1_2mm_brain_mask as well
as the float images like zstat.
All the best,
Mark
P.S. Note that the kernels in fslmaths sum to 1, and hence their
individual voxel values are less than one.
Martin M Monti wrote:
> John,
>
> ha, that's true. On the other hand, try that same syntax with a
> thresh_zstat*.nii.gz image. Does it work? (It does on my side --
> provided the voxel you pick is active in the thresh_zstat you pick..).
>
> So I dunno what the problem is, but I'd presume something to do with
> the voxel size or resolution and the like?
>
> let me know if that works..
>
> for completeness, here is the syntax I've been successfully using (all
> the $... are just variabls, so ignore them..):
>
> fslmaths ../thresh_zstat1.nii.gz -roi $x 1 $y 1 $z 1 0 1
> ${sub}_SMA_sphere
> fslmaths ${sub}_SMA_sphere -kernel sphere 10 -fmean ${sub}_SMA_sphere
>
> fslmaths ${sub}_SMA_sphere -bin ${sub}_SMA_sphere
>
> cheers
>
> martin
>
>
> John Herrington wrote:
>> 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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