[Mristudio-users] ROI Editor Questions

[John Migliozzi]

Thank you.  I have another question as well:  In Landmarker, I would like to
preform multichannel LDDMM, between my data and some of the Atlas Sample
Data, but none of the Atlas Sample Data has parameters that match my data.
Is there a way that I can adjust the sample data (or my data) so that they
both have the same paramters?

Thanks,
John

On Wed, Jun 3, 2009 at 7:07 PM, susumu mori <susumu at mri.jhu.edu> wrote:

> 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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