[Mristudio-users] [Fwd: short course]

[Susumu Mori]

Hi Steen, I want to ask several questions;

1) Do you have a atlas mouse image? I guess you already have one.
2) Do you have a structure-definition (ROI) file that defines various
structures in the atlas I mentioned above (#1). If so, where did it come
from? How many structures are defined?
3) If you could successfully transform subject->atlas or atlas->subject, it
is straightforward to apply the transformation matrix to the ROI file (#2).
If the resolution of the subject and atlas are different, the
transformation is most likely two-step: first AIR (linear) and then
non-linear (LDDMM). These two matrices can be combined to achieve one-shot
transformation. This process is described in the "Getting Started" at
https://www.mristudio.org/wiki/user_manual/diffeomap.
4) This transformation should preserve the object list information (as Xin
mentioned) but as long as you have a look-up table, you can always decode
the meaning of the Object numbers. Please make sure to use "nearest
neighbor" interpolation for the ROI file. The assigned number for each
structure is arbitrary. You don't create "Object #2" in between "Object #1"
and "Object #3" after the ROI file warping.

Please let me know if you have further questions.

Susumu


On Tue, Jan 21, 2014 at 5:55 PM, Pedersen, Steen E. <
sepeders at texaschildrens.org> wrote:

>  Dear Support
>
>                 First, thanks for writing such a powerful and useful set
> of programs. I have a question regarding the mouse brain atlas maps.
>
>
>
> The segmentation of the mouse brain appears very useful. I am processing
> data from a number of users doing mouse brain. Unfortunately, for each
> experiment, the exact dimensions of each set of scans can vary as can the
> mouse age.
>
>     I have been using the mouse atlas for registration to a standard mouse
> so as to compare groups of mice objectively. This is fine, and I can
> resample the standard mice easily in diffeomap.
>
>                 My question is whether there is a simple way to resample
> the segmentation maps for the mouse brain. This would give me a powerful
> way to quickly get detailed information back to the user. I can resample
> the raw ROI data, but I lose the label information (ei – the objects become
> “object 1, object 2, etc” instead of “hippocampus-L, hippocampus-R, etc”.
>
> Other than typing it in each time, is there a way to import the labels
> into ROIeditor to get them back? I have tried using a new header, but it
> doesn’t seem to preserve the object labels.
>
>
>
> If there is a more detailed manual for ROIeditor, I would greatly
> appreciate a pointer for it as I see it being a very useful tool for my
> work.
>
>
>
> Thank you,
>
> Steen Pedersen
>
> (registered email: pedersen at bcm.edu)
>
>
>
> Steen E. Pedersen, Ph.D.
>
> Associate Professor
>
> Small Animal Imaging Facility
>
>
>
> Phone: 832-824-3399
>
> Cell: 713-726-0041
>
> email: sepeders at texaschildrens.org
>
>
>
> Feigin Center, Room C.0200.02
>
> Texas Childrens Hospital
>
> 1102 Bates St., Houston, TX 77030
>
>
>
> *éala éarendel engla beorhtast*
>
>
>
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