[Mristudio-users] 3D ROI

[susumu mori]

Hi Bin,

To save a file as "Binary Map", you have to open it as ROI, not as an image.
There are two "open" icons in the right column of RoiEditor; one for image
and the other for ROI.

To access to these icons, you first have to open an image. The image can be
anything as long as it has the same image dimension. For example, you can
open the ROI file as an image, get the viewing window, and then open the
same file as an ROI file.

Then you can save the ROI as "Binary Map".

Susumu



2011/2/28 bin wang <binwang87828 at gmail.com>

> Dr Mori:
> Thank you for the patience to answer, I will try as you say.
> But there is still a question that I can't save it as "Binary Map" after
> loading the mask image to RoiEditor, I must draw a ROI manually or using
> other ways. I want to know that can I make the mask as a ROI directly, so
> the ROIEditor can save it.
> Best
> bin
>
> 在 2011年2月27日 下午7:31，susumu mori <susumu at mri.jhu.edu>写道：
>
>
>>
>> 2011/2/27 bin wang <binwang87828 at gmail.com>
>>
>> Dr Mori:
>>> I have two questions:
>>> (1). If I want to create a 3D ROI, Must I draw the ROI in every slice in
>>> ROIEditor manually?
>>>
>>
>> If the structure of interest has clear contrast, you can use a region
>> growing tool. For example the caudate in T1 has a good contrast. You can use
>> 3D or slice-by-slice region growing tool to define it much easier than
>> manual. When you are using DTI colormap, there is a color region growing
>> tool to specify a region with the same color.
>>
>> If does not have clear contrast, you can first use the global threshold or
>> region growing to define a tissue of interest. For example, if you are
>> interested in a white matter structure, you can use FA>0.25. If you are
>> interested in the cortex, you can use a threshold tool with T1. Please note
>> that white matter structures and the cortex do not have clear contrast
>> boundary from adjacent structures. Therefore the region growing or
>> thresholding almost always leak to adjacent structures. After you do the
>> global tissue segmentation, you can visit each slice and use manual ROI +
>> AND operation to define the structure.
>>
>> If you get tired of defining a lot of ROIs without clear boundaries,
>> please try our automated full-brain segmentation tools. You need to learn
>> how to use DiffeoMap and RoiEditor. You can find manuals and videos in
>> www.mristudio.org.
>>
>>
>>
>>> (2). I have a binary mask image(img/hdr), it is the calcarine regions of
>>> the brain, I want to make a ROI of the region to track the fiber in this
>>> region, and how can I do in ROIEditor or DTIstudio.
>>>
>>
>> You can load it to RoiEditor as an ROI file and save as "Binary Map".
>> Please refer to FAQ16 about Binary Map format.
>>
>>
>>> Thanks in advance
>>> Bin
>>>
>>> 在 2011年2月27日 上午12:10，susumu mori <susumu at mri.jhu.edu>写道：
>>>
>>> Yes, RoiEditor can draw 3D ROIs. Because the ROI drawing capability of
>>>> DtiStudio is limited, I recommend to use RoiEditor. It is possible to create
>>>> multiple 3D ROIs in RoiEditor and pass them DtiStudio for fiber tracking.
>>>> Please refer to FAQ16 in https://www.mristudio.org/wiki/faq.
>>>>
>>>> 2011/2/26 bin wang <binwang87828 at gmail.com>
>>>>
>>>>>  Hello DTIstudio user:
>>>>> I am a new DTIStudio user, I want to know if the ROIEditor can drawing
>>>>> a 3D ROI, and how to operation?
>>>>> bin
>>>>>
>>>>> --
>>>>> ++++++++++++++++++++++++++++++
>>>>> Bin Wang
>>>>> major：apply psychology
>>>>> South China Normal University
>>>>> Zhongshan Avenue West 55, Tianhe District
>>>>> Guangzhou 510631
>>>>> P. R. China
>>>>> Tel: 13416157706
>>>>> ++++++++++++++++++++++++++++++
>>>>> 王斌
>>>>> 华南师范大学
>>>>> 应用心理专业
>>>>> * 地址：
>>>>> *广东省 广州市 天河区 中山大道 西55号
>>>>> 邮编：510631
>>>>> 电话： 13416157706 (手机, 广州)
>>>>> +++++++++++++++++++++++++
>>>>>
>>>>>
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>>>
>>>
>>> --
>>> ++++++++++++++++++++++++++++++
>>> Bin Wang
>>> major：apply psychology
>>> South China Normal University
>>> Zhongshan Avenue West 55, Tianhe District
>>> Guangzhou 510631
>>> P. R. China
>>> Tel: 13416157706
>>> ++++++++++++++++++++++++++++++
>>> 王斌
>>> 华南师范大学
>>> 应用心理专业
>>> * 地址：
>>> *广东省 广州市 天河区 中山大道 西55号
>>> 邮编：510631
>>> 电话： 13416157706 (手机, 广州)
>>> +++++++++++++++++++++++++
>>>
>>>
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>>
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>
>
> --
> ++++++++++++++++++++++++++++++
> Bin Wang
> major：apply psychology
> South China Normal University
> Zhongshan Avenue West 55, Tianhe District
> Guangzhou 510631
> P. R. China
> Tel: 13416157706
> ++++++++++++++++++++++++++++++
> 王斌
> 华南师范大学
> 应用心理专业
> * 地址：
> *广东省 广州市 天河区 中山大道 西55号
> 邮编：510631
> 电话： 13416157706 (手机, 广州)
> +++++++++++++++++++++++++
>
>
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> mristudio-users mailing list
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> http://lists.mristudio.org/mailman/listinfo/
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