[Mristudio-users] FW: Using ROI editor

[susumu mori]

Hi Nida,

I hope #7 and #11 in the "Getting Started" of this page (
https://www.mristudio.org/wiki/user_manual/diffeomap) answer some of your
questions.

Because you did 3-alpha transformation, you get Ki001/Ki002/Ki003 and
Kimap. Ki001-003 are recorded for each alpha step. For example, if you did
alpha = 0.01/0.005/0.002, Ki001 gives you a transformation with alpha=0.01.
If you combine Ki001+Ki002, then you can create an image after alpha =
0.01+0.005. Ki001+002+003 = Kimap. So, if you want a result after all three
iterations of different alpha values (elasticity), you simply use Kimap.

If you use Kimap, your patient images become similar to our atlas. If you
superimpose our WMPM (changed the name to BPM recently) and if the
transformation is successful, you should see accurate parcellation.

Conversely, you can transform BPM by using Hmap (as explained in the #11
above), you need to use nearest neighbor for this transformation. In this
way, the parcellation map is transformed to the shape of the patient in the
native space.

If you see poor matching between the image and the parcellation map, common
mistakes are;

> transformation was not accurate because the initial linear registration
results are poor. You may need to do skull stripping or landmark-driven
initial alignment. Our Mutual Information option, instead of AIR, often
performs better.
> you used Hmap, not Kimap to the patient image and applied the atlas-space
BPM or you used Kimap, not Hmap, to the BPM and applied to the native space
patient image.

If you send me an image showing how bad the parcellation by BPM, I may be
able to tell why.


On Sun, May 12, 2013 at 10:47 AM, Nida Sajjad <nidasajjad958 at hotmail.com>wrote:

>
>
> ------------------------------
>
>
> Dear All,
>
> I am sorry may be i am not able to explain my problem exactly. The data
> you are seeing in attached files is just from some tutorial its not my
> original data. i was just trying to explain that  i am following thee steps
> as mentioned in the pictures. After multichanel processing of my data, i
> got results which contain following files:
> finalMetricDistance,
> Hmap.vtk,
> Hmap_001.vtk
> Hmap_002.vtk
> Hmap_003.vtk
> ,identity,
> Kimap.vtk
> Kimap_001.vtk
> Kimap_002.vtk
> Kimap_003.vtk
> lddmm-vmm1.conf
> lddmm-vmm2.conf
> lddmm-vmm3.conf
> LocalAddress
>  stdout
> Target1.img
> Target2.img
> Template1.img
> Template2.img
> Now when i want to use my Updated FA in Roi editor and upload Rois they
> are not fully fit to my data. How can i use the above mentioned processed
> data in Roi editor. This is what i want to ask. And also that the roi
> statistics contain pixel value , min max and mean and std deviation. Are
> these the FA values for each Roi?
>
> I hope now i am able to make my self clear.
> Thank you much
>
> Regards,
> Nida
>
>
>
>
>
>
>
> ------------------------------
>
>
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