[Mristudio-users] Atlas based analysis using LDDMM

[susumu mori]

Well, if you could show me the image, I may be able to help you better, but
one thing I can tell now is, when you transform a WMPM, you need to use
"nearest neighbor". Each ROI in the WMPM contains artificially assigned
numbers; say, ROI-A is 12 and adjacent ROI-B is 20. If you transform this
map using trilinear, it would generate the number "16" right in the middle
of the region A and B, but the number 16 may be assigned to a totally
unrelated ROI.

So, please try nearest neighbor and see how it goes.

On Tue, Oct 11, 2011 at 9:33 PM, manoj sarma <mksarma at gmail.com> wrote:

> Hello DTI Experts,
>
> I am trying to do an atlas based analysis using LDDMM. My goal is to do an
> anlysis on my FA/MD map such as done in
> http://www.ncbi.nlm.nih.gov/pubmed?term=20570617 (paper by Zhang).
> Therefore, I have used the steps described in
> https://www.mristudio.org/wiki/user_manual/diffeomap.
>
> I first processed the DTI data using 'DTI-Studio' and then skull stripped.
> To obtain the AIR and LDDMM transformation matrices
>  I co-registered my skull stripped FA/MD/B0 map with 'JHU_MNI_SS_b0_ss'
> template using AIR and then used 'FA + b0 dual-contrast LDDMM' with
> 'JHU_MNI_SS_b0_ss' and 'JHU_MNI_SS_FA_ss' templates.
>
> After obtaining the LDDMM matrix, I apply the Hmap to the
> 'JHU_MNI_SS_WMPM_TypeII' template. But it looks to me the image I got is
> having some problem. I am not sure if doing some mistakes. I used trilinear
> interpolation for Hmap.
>
> Can anyone please tell me if I am following the correct procedure? Where I
> may go wrong?
>
> Thanks in advance,
> Manoj
>
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