[slicer-users] Black noise artifact on Joint Rician LMMSE filter and resample DWI to isovoxel

David Qixiang Chen qixiang.chen at gmail.com
Thu Aug 5 12:50:06 EDT 2010


Hi Steve,
I just tested this with the tutorial data, no black spots.
Have you tried it on my sample data? I'm on a 64bit system btw.

Looks like it's limited to my scans. Could this be due to the large
number of directions I have? Our scans are usually done with either 25
directions or 60 directions.

Thanks,

- David

On Thu, Aug 5, 2010 at 12:39 PM, Steve Pieper <pieper at bwh.harvard.edu> wrote:
> Hi David -
>
> Can you try with the dwi data from the tutorial?
>
> http://www.slicer.org/slicerWiki/images/c/cf/DiffusionDataset.zip
>
> I just tested this and didn't get any black spots.  I'm thinking the issue
> may be overflow related to the dwi values in a particular dataset.
>
> -Steve
>
> On Aug/5/10 11:42 AM, David Qixiang Chen wrote:
>>
>> Hi Demian,
>>
>> This is consistently reproducible for me since the Joint Rician LMMSE
>> filter was introduced.
>> I've reproduced this in 3.7 alpha now.
>>
>> I use the default settings:
>> estimation radius: 2,2,1
>> filtering radius: 2,2,1
>> # of neighboring gradients: 0
>>
>> If you look at the individual gradients of the DWI volume, the black
>> specs are always there.
>> Can you tell me what settings you used? If you can't reproduced this,
>> that certainly is good news.
>>
>> - David
>>
>> On Tue, Jul 27, 2010 at 7:20 AM, Demian Wassermann
>> <demian at bwh.harvard.edu>  wrote:
>>>
>>> Hi David,
>>>
>>> I've been looking at your data trying to reproduce the problem and I
>>> wasn't able to.
>>>
>>> Could you give me more details? Slicer version, filter that you are
>>> using, etc etc
>>>
>>>
>>> Thanks
>>> Demian
>>>
>>>
>>> --
>>> Demian Wassermann, PhD
>>> demian at bwh.harvard.edu
>>> LMI / PNL / SPL Labs
>>> Harvard Medical School
>>> Brigham and Women's Hospital
>>> 1249 Boylston, Boston, MA, USA
>>>
>>> On Jul 19, 2010, at 11:24 AM, David Qixiang Chen wrote:
>>>
>>>> Hi Damian,
>>>>
>>>> Here's the eddy corrected scan using tend epireg.
>>>> http://drop.io/eyqpfyi
>>>> http://drop.io/y0ydghc
>>>>
>>>> Btw any ideas about doing isovoxel resampling on DWI images?
>>>>
>>>> Thanks,
>>>>
>>>> - David
>>>>
>>>> On Sat, Jul 17, 2010 at 2:08 PM, Demian Wassermann
>>>> <demian at bwh.harvard.edu>  wrote:
>>>>>
>>>>> Hi David,
>>>>>
>>>>> How are you doing?
>>>>>
>>>>> Is there a way I can get the nrrd file of your DWI image? I would like
>>>>> to analyze it to help you
>>>>>
>>>>> Thanks
>>>>> Demian
>>>>> --
>>>>> Demian Wassermann, PhD
>>>>> demian at bwh.harvard.edu
>>>>> LMI / PNL / SPL Labs
>>>>> Harvard Medical School
>>>>> Brigham and Women's Hospital
>>>>> 1249 Boylston, Boston, MA, USA
>>>>>
>>>>> On Jul 17, 2010, at 11:54 AM, Ron Kikinis wrote:
>>>>>
>>>>>> <Attached Message Part.txt>
>>>>>
>>>>>
>>>
>>>
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