Hi Christian,
There should not be a normalization, you would explicitly ask for this
by the -inm or -ing argument.
Try to compare your stats with fslstats using lower case -r (i.e. get
the robust min max estimates). It might be that the extreme values from
the original image are way off and only a few voxel show these extreme
values and thus average out.
The other option to check would use -Zmin and -Zmax to get an idea of
the range of values within the slab.
wolf
On 07/05/2018 11:32 AM, Christian Rubbert wrote:
> Dear Wolf,
>
> thank you very much. Apparently I had overlooked '(the "T" can be
> replaced by X, Y or Z to collapse across a different dimension)' in
> the fslmaths help...
>
> However, the slabs' mean values are way off what I would expect. I'm
> using brain CT scans, so the minimum voxel values (in Hounsfield
> units) outside of the brain should be around -1000 (for surrounding
> air) and the maximum values should be well over 1000 (e.g. for
> cortical bone). The min and max values of my input file are accordingly
>
> $ fslstats dcm-in_5_CCT_5_Tilt_1.nii.gz -R
> -1513.847290 2485.602539
>
> Whereas the mean values for the slabs are:
>
> $ for i in 5mm/slab_*; do fslstats $i -R; done
> -53.894737 90.442108
> -53.894737 98.136841
> -53.894737 117.305260
> -53.894737 114.726318
> -53.894737 106.305260
> -53.894737 105.357895
> -53.894737 98.831581
> -53.894737 106.968422
> -53.894737 106.452629
> -53.894737 98.263161
> -53.894737 92.368423
> -53.894737 90.073685
> -53.894737 89.621056
> -53.894737 72.631577
> -53.894737 66.715790
> -53.894737 65.515793
> -53.894737 63.252632
> -53.894737 61.536842
> -53.894737 26.473684
>
> is there anything I am overlooking? Some kind of normalization?
>
> Thank you & best regards,
> Christian
>
>
>> Date: Wed, 4 Jul 2018 00:41:02 -0500
>> From: wolf zinke <[log in to unmask]>
>> Subject: Re: Generating a mean slab?
>>
>> I guess with some scripting:
>>
>>
>> flname="yourfile"
>>
>> SlabThick=5
>>
>> Xdim=$(fslval $flname dim1)
>>
>> Ydim=$(fslval $flname dim2)
>>
>> Zdim=$(fslval $flname dim3)
>>
>>
>> MaxZ=$(($Zdim-$SlabThick))
>>
>>
>> for cZ in $(seq 0 $SlabThick $MaxZ)
>> do
>> fslmaths $flname -roi 0 $Xdim 0 $Ydim $cZ $SlabThick 0 1 -Zmean
>> Slab_${cZ}
>> slicer Slab_$cZ -z 0 Slab_${cZ}.png
>> done
>>
>>
>> good luck,
>> wolf
>>
>>
>> On 07/04/2018 12:17 AM, Christian Rubbert wrote:
>>> Hey FSL-users,
>>>
>>> is it possible to calculate a mean image slab (e.g. combining five 1
>>> mm slices to a single 5 mm slab, which is the mean of the voxels of
>>> the 5 slices only in the z-direction) using FSL? Ideally I would
>>> like to generate such a mean slab every 5 mm over a whole volume.
>>>
>>> Thank you very much!
>>>
>>> Best regards,
>>> Chrisitan
>
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