[Mristudio-users] ROI Editor Questions

[susumu mori]

Hi John,

Xin can answer some questions better than me, but let me answer some
questions;

1: Add / Subtract / Multiply / Divide: you need to load at least two images
into one window. The first image needs to be loaded using the "open" icon in
the upper menu bar and the second from the "open" icon in the right column
of the viewing window. Once two images are loaded, you should see them
listed in the pull-down menu in the right column. If you have more than 2
images, you can use this function for addition / subtraction /
multiplication / division. The T2 option can calculate a T2 map from
multiple T2-weighted images. For example, if you have two images with TE =
40 and 100 ms, you can load them into one window. If you choose the T2
option, another window pops up for you to specify the echo times. Then, you
can calculate a T2 map.

3: You can select pixels based on thresholding. For example, you can load an
FA map and specify pixels between 0.3 and 0.8 using this button. Then you
can register such pixels as an ROI.

4: Skull stripping: I agree that there are too many parameters. There are
single and multi-contrast options. For the single-image option, it is
basically a automate region-growing. It is like you start to blow a balloon
from the center of the image. The balloon stops expanding when it hits the
brain boundary (large intensity change between the brain and skull). Then
the balloon stops growing when it becomes the shape of the brain. In this
way, it can automatically define the boundary of the brain and thus can
remove the skull. Some of the parameters can control the softness of the
balloon. If the balloon is too stiff, it can not accurately trace the brain
shape. If it's too soft, it can leak to connected structures such as the
skull and eyeballs. You can use aDWI (average of all DWIs) or b0 with the
single-image skull stripping. With the default values, it should work. These
images usually has very faint skull intensity and skull removal should be
straightforward.

For the dual-image option, you can specify b0 or aDWI (with which the skull
strip is easy) and T1 or T2 anatomical images (with which the skull strip is
difficult). It first does the single-image skull strip using b0 or aDWI.
Then the defined brain boundary is transferred to T1 or T2 anatomical
images. Here, the T1 and T2 must be coregistered with b0 (or aDWI) and has
the same dimension by going through our registration software (Landmarker).
Because b0/aDWI often has image distortion (and also registration errors),
the simple transfer of the brain boundary defined by b0 (or aDWI) is not
accurate. This software then searched the nearest brain boundary by
massaging the initial shape. We had some success to skull-strip
co-registered T2-weighted anatomical images using this function, but it is
still work-in-progress. That's why all the parameters are available for us
to do parameter setup.

5: Export Pixel value: This is to create a histogram. Once you define an
object (ROI), you can get a report of pixel intensity averaged over all
pixels inside the ROI. However, you may not want such average and want to
know the distribution of values of all pixels in the ROI. In this case, you
can export the pixel values as a text file, read by Exel, and create a
histogram.

Susumu

On Wed, Jun 3, 2009 at 12:56 PM, John Migliozzi <john.migliozzi at gmail.com>wrote:

> Hi everyone,
>
> I'm working with ROI Editor, and I have a few questions regarding some
> features of the program.
>
> 1.  Operations.  I understand how mask works, but cannot figure out the
> add, subtract, multiply, divide, and T2
> 2.  Change ROI File Header.
> 3.  Threshold.
> 4.  Skull Stripping.  I cannot figure out how to appropriately adjust these
> parameters.
> 5.  Export Pixel Value option when you right-click on an object.  What do
> the numbers in the text file mean?
>
> Also, I am having a problem when I try to import ROIs from ROI Editor back
> into DTI Studio.  Regardless of what format in which I export the data, DTI
> Studio tells me it is an "unrecognized Image-ROI data file."
>
> If anyone can answer any of these questions, I would be really
> appreciative.
>
> Thanks,
>
> John Migliozzi
> john.migliozzi at gmail.com
>
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