Hi Ged,
Thanks a lot, that definitely helps, everything works as expected now!
Best,
Stephane
Ged Ridgway wrote:
> Stephane Jacobs wrote:
>> I'm trying to improve the result of skull-stripping by playing a
>> little bit
>> with the options of bet.
> ...
>> option to set the starting point of the algorithm to a point closer
>> to the
>> actual "center" of the brain.
> ...
>> /blabla/anat1 bet 0000653_1_4.nii 653_try -c 4 -53 -19
>
> Hi Stephane,
>
> I think the -c option expects "scaled" mm coordinates, rather than
> NIfTI "world" mm coordinates from fslview. These are the voxel
> coordinates multiplied by the (unsigned) pixel dimensions. (so they
> must be positive, unlike the world coords you appear to be using).
>
> For the radius, I'd try something much bigger than 5mm, based on a
> rough estimate from moving the cursor from one side of the brain to
> the midpoint in fslview.
>
> Hope that helps,
> Ged.
>
>
--
Stephane Jacobs
Human Neuroimaging and Transcranial Stimulation Lab
36 Straub Hall, 1227 University of Oregon
Eugene, OR 97403 - USA
Email: [log in to unmask]
Tel: (1) 541-346-4184
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