[Mristudio-users] DTI normalization with Diffeomap on lesioned brains

[Dorian P.]

Thank you Dr. Mori,

Yes, my lesions are mostly surgical resections. The second question was
mostly a comparison between different alpha maps in LDDMM and SPM
normalization on lesioned brains. In SPM a T1 can be normalized (either
directly or through segmentation) on a MNI template and the transformation
matrix can be applied to any volume (i.e. BOLD, FA, Tensors). I was
wondering whether this method maybe worst or better on lesioned data
compared to LDDMM.

Best regards.
Dorian

2012/12/1 susumu mori <susumu at mri.jhu.edu>

> You need to mask anatomically equivalent regions in both the patients and
> the atlas, which is difficult.
> I assume your "lesions" mean surgically removed tissues. Is it correct? If
> you can assume that the anatomical deformation around the lesions is small
> (like the partial moon), you can register the patient image to the atlas by
> affine (either automatically or landmark-driven) and transfer the lesion
> locations to the atlas manually, I think. In stead of affine, you may be
> able to use low-elasticity LDDMM (alpha = about 0.01).
>
> I didn't quite get your second question. Using LDDMM (DiffeoMap), you can
> control the elasticity by alpha value. 0.01 and larger give low elasticity.
> 0.005 is recommended for normal brains. 0.001-0.002 is used when anatomical
> difference is large.
>
> When you want alpha smaller than 0.005, cascading alphas are recommended
> (e.g. three consecutive LDDMM with 0.01-0.005-0.002) to avoid being trapped
> by a local minima. Using this cascading-alpha approach, you can also obtain
> the intermediate results; results with low elasticity (alpha = 0.01),
> medium alpha (alpha = 0.01/0.005).
>
> In DiffeoMap, you can use up to 3 cascading alphas.
>
>
> On Fri, Nov 30, 2012 at 7:54 PM, Dorian P. <alb.net at gmail.com> wrote:
>
>> Thank you for answering Dr. Mori,
>>
>> Would it be feasible to mask only the lesion on the patient or does it
>> have to be on both patient and atlas?
>>
>> Has anybody compared a T1 normalization on SPM and applying the matrix to
>> DTI to a low elasticity normalization in DTIstudio?
>>
>> Best regards.
>> Dorian
>>
>>
>> 2012/11/30 susumu mori <susumu at mri.jhu.edu>
>>
>>> In general, lesions (severe intensity changes) or severe anatomical
>>> changes (e.g. missing tissues or tumor) are very difficult to deal with,
>>> when you are using a transformation-based analysis.
>>>
>>> When you use transformation with low elasticity (e.g. linear
>>> transformation), the transformation could be less affected because the
>>> registration would be mostly driven by the brain outlines. So, if your
>>> lesions (intensity changes) do not accompany anatomical deformation, you
>>> may be able to compare patients and controls.
>>>
>>> As the elasticity increases, the transformation would be more affected
>>> by the lesions. Of course, if the lesions are small, they may not cause
>>> much problems but I assume you have large lesions.
>>>
>>> If you are studying, for example, stroke and interested in anatomical
>>> changes of contralateral hemisphere (or the brainstem), you can mask-out
>>> the ipsilateral hemisphere for both patients and the atlas. We have done
>>> this type of analyses before.
>>>
>>> Sorry that I could give you only a generic answer. This is an issue that
>>> the whole community faces.
>>>
>>> On Fri, Nov 30, 2012 at 2:52 PM, Dorian P. <alb.net at gmail.com> wrote:
>>>
>>>> Hi all,
>>>>
>>>> I am interested on normalizing lesioned brains with a dual channel
>>>> Diffeomap procedure. The normalization will be done on MNI existing
>>>> template of Diffeomap. Lesions typically come from surgical resections.
>>>>
>>>> Does this procedure work well on lesioned brains or shall I need some
>>>> mask for Diffeomap to avoid normalizing the lesioned area?
>>>>
>>>> Any comment is welcome. I couldn't find much about the topic on
>>>> previous posts and articles.
>>>>
>>>> Thank you.
>>>> Dorian P
>>>>
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