[Mrtrix-discussion] question about CSD

[Olivier.Salvado at csiro.au]

I agree with your point and I actually raised it during the talk I mentioned. It is a bit fuzzy as it was long time ago though, so I am not sure to remember correctly, let alone to provide some meaningful insights. I discussed that issue with Steve Rose after the talk and we agreed that anisotropy would bias tractography. But to be honest I am struggling now to remember my train of thoughts to reach that conclusion...

If resolution along Z is lower then you could expect more partial voluming, thus a flatter FOD along that direction. Therefore any tractography going through the Z direction would be prone to stop (not enough diffusion) or shoot in spurious directions for lack of sharply defined major axis. On the other hand, the inplane resolution would have lower SNR so the FOD might be sharper but shooting in random directions as well...

Perhaps you could communicate with the speaker, he was keen on getting suggestions and discussing his work. 

Cheers
Olivier
____________________
Olivier Salvado, PhD
Group  Leader | Biomedical Imaging
ICT, The Australian e-Health Research Centre
CSIRO
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-----Original Message-----
From: mrtrix-discussion-bounces at www.nitrc.org [mailto:mrtrix-discussion-bounces at www.nitrc.org] On Behalf Of Michael Zeineh
Sent: Tuesday, 19 January 2010 15:00
To: 'Donald Tournier'
Cc: mrtrix-discussion at www.nitrc.org
Subject: RE: [Mrtrix-discussion] question about CSD

The reason you think it would be better through plane is what ... Better SNR
(I would think SNR just depends on overall voxel size)? Less eigenvector
error for some other reason?

Let me pose it more specifically. Say our in-plane resolution is say 1mm,
and our thru plane resolution is 5mm. Let us say the white matter structure
has detail along two but not three of its dimensions that could not be
resolved at 5mm resolution but could be resolved at 1mm resolution. Along
the third dimension, it could be resolved at lower resolution. In this case,
one would definitely want the orientation such that the two dimensions
requiring the resolution are the in-plane orientation with higher
resolution, I would think.

Olivier, it would be great to get the insight from the talk if this issue
was addressed.

-----Original Message-----
From: Donald Tournier [mailto:d.tournier at brain.org.au] 
Sent: Sunday, January 17, 2010 8:30 PM
To: Michael Zeineh
Cc: mrtrix-discussion at www.nitrc.org
Subject: Re: [Mrtrix-discussion] question about CSD


Hi Michael,

Actually, I would have thought it would be the opposite: a structure
entirely through plane would be resolved better. That said, I can't think of
any studies that have looked at that specifically, so don't quote me on
that... Maybe someone else on the list can suggest an appropriate
reference...?

Cheers,

Donald.


2010/1/18 Michael Zeineh <mmzeineh at gmail.com>:
> Thank you Donald.
>
> I see. So, for the example an axial DTI with thick slices but small in 
> plane voxels, a structure entirely in-plane would be resolved better 
> than if the same object were entirely through-plane (assuming things 
> like SNR are similar).
>
> Michael
>
> On Sun, Jan 17, 2010 at 3:18 PM, Donald Tournier 
> <d.tournier at brain.org.au> wrote:
>> Hi Michael,
>>
>> Yes, it should work with anisotropic voxels (although isotropic would 
>> always be recommended). There is little point interpolating (at least 
>> not using linear interpolation), since the tracking code performs 
>> linear interpolation while tracking. In terms of bias, the 
>> orientations are provided with respect to real (scanner) coordinates, 
>> so do not depend on the voxel dimensions. There would however be a 
>> bias when tracking WM structures oriented predominantly through-plane 
>> versus in-plane, since the "effective resolution" would be higher in 
>> the first case. This applies to all tracking methods though, not just 
>> MRtrix (and is not a limitation of the CSD itself).
>>
>> Hope that helps,
>>
>> Donald.
>>
>>
>> 2010/1/16 Michael Zeineh <mmzeineh at gmail.com>:
>>> Out of curiosity, will it work on anisotropic diffusion data (i.e. 
>>> voxels are thicker along one axis)? If so, would there be any 
>>> expected errors or biases? Would simple interpolation (somewhat) 
>>> resolve those issues?
>>>
>>> Thank you,
>>> Michael
>>> _______________________________________________
>>> 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
>>
>



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

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