[Mristudio-users] ROI Editor Questions

Thu Jun 4 20:13:29 EDT 2009

please go over https://www.mristudio.org/wiki/user_manual/landmarker and
follow Step one-two-three. For the first step, you can choose any ICBM-152
based atlas (JHN-MNI-GA, JHU-MNI-SS, ICBM-DTI-81). After Step 1, not only
the brain location and orientation become similar to the atlas, but also he
matrix and pixel size become the same; 181x217x181 / 1x1x1 mm. This
pre-conditioning is necessary to do LDMM (Step 2).

On Thu, Jun 4, 2009 at 10:47 AM, John Migliozzi <john.migliozzi at gmail.com>wrote:

> 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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>>
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