[Mrtrix-discussion] voxel editing

[Donald Tournier]

Hi Kerstin,

Strange indeed.... If you want to use fslview, here's a trick that
might conceivably help: use mrconvert to create the NIfTI image that
you will be drawing on, and load that in fslview to draw your ROIs.
I've found in the past that fslview doesn't handle NIfTI images that
have non-standard data orderings very well - i.e. if the image is
stored as a stack of sagittal slices, it displays in the "wrong"
orientation. This is a problem particularly with overlays if the two
images are ordered differently. I'm guessing this problem will extend
to ROIs as well since that is a form of overlay. If you convert the
image using mrconvert, it will guarantee that the image is stored as a
stack of axial sices - i.e. the transform is close to the identity.
Not sure I'm making sense, but it might be worth a shot.

Another tool that you might be interested in is mricron - I've just
had a play with it, and it seems to work OK.

Hope that helps.

Donald.


On Tue, Nov 3, 2009 at 2:12 PM, Kerstin Pannek <k.pannek1 at uq.edu.au> wrote:
> Hi Donald
>
> unfortunately that didn't work.
> Attached is a screenshot that might explain the problem we are having a bit
> better. Basically we can edit in about 3/4 of the brain, and then it just
> ends...
>
> I tried using fslview for drawing ROIs, but it does some funny flipping when
> it saves the ROI
>
> Cheers
> Kerstin
>
>
> Donald Tournier wrote:
>>
>> Hi Kerstin,
>>
>> Yes, mrview is not great for drawing ROIs. A better version is on my
>> to-do list...
>>
>> There are often subtle alignment issues between the original image and
>> the overlaid ROI. The problem is that the software tries to fill in
>> the voxel at the current focus (crosshairs), and sometimes the
>> crosshairs are right on the border between two voxels, causing some
>> voxels to update and other not according to round-off. This can be
>> very hard to spot, since the focus is a point in 3D space, so
>> mis-alignment can happen through-plane. Try this:
>> - turn off interpolation (View->Interpolate)
>> - display the image in a different plane (i.e. go from axial to sagittal,
>> etc)
>> - make sure the crosshairs are in the middle of a voxel
>> -  go back to the projection you were drawing on, and try to fill in
>> those voxels you were having trouble with.
>>
>> Let me know if that doesn't help...
>> Cheers,
>>
>> Donald.
>>
>>
>> On Tue, Nov 3, 2009 at 9:18 AM, Kerstin Pannek <k.pannek1 at uq.edu.au>
>> wrote:
>>
>>>
>>> sorry if you received this email twice...
>>>
>>> --------
>>>
>>> Hi all
>>>
>>> we are having some trouble drawing ROIs on a mouse brains here. That is,
>>> mrview allows us to only fill in or delete voxels in about 2 thirds of
>>> the
>>> imaging volume, with a sharp line between editable and uneditable voxels
>>> in
>>> the left-right direction.
>>> We tried on 64 bit Ubuntu Hardy and 32 bit Ubuntu Jaunty.
>>>
>>> Any help on this would be greatly appreciated.
>>>
>>> Cheers
>>> Kerstin
>>> _______________________________________________
>>> Mrtrix-discussion mailing list
>>> Mrtrix-discussion at www.nitrc.org
>>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>>
>>>
>>
>>
>>
>>
>
>



-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9496 4078