[Brains-users] class image 2 descrete - rule of thumb?

[Eugene Zeien]

The "Measure Image Mask" function applies the selected mask to
the selected image for measurement purposes.  Masks and images
are separate entities within Brains until the operator chooses
a function which combines them.  The result of almost all such
operations is a new object (mask, image).  The original mask and
image are unaffected.

Christoph Christmann wrote:
> 
> I see. I think we will threshold the segmented image manually in order 
> to find grey/white border regions difficult to identify in usual T1 or 
> T2 images (for example the border between amygdala and hippocampus). 
> This seems to work pretty well.

Yes.  Manually delineating an ROI (region of interest) is a superior method.
Especially in those areas where the boundaries are difficult to see.

> However, thresholding masks unfortunately apply for any image actually 
> loaded (e.g. the T1 and T2). Do you see a possibility to apply a mask 
> only for a single loaded image (e.g. the segmented)?

When masks are loaded or created, Brains displays the mask "over" any
image in the viewing area.  The mask is not actually applied until you
choose an action such as "Measure Image Mask" or "b2 clip image".  To
hide the masks, click on the [Selector] button on any image view window.
Click on the mask you wish to hide in the "Object" area, then click
[Display] click again to enable display.  To hide all the masks, type
	b2 hide every mask
in the terminal where you started brains2.

> 
> TIA
> 
> christoph
> 
> At Thursday 09.03.2006 22:34, you wrote:
> 
>> Converting a segmented image to a discrete image is a simple
>> matter of applying thresholds.  Using the menu item from the
>> brains2 toolbar applies a talairach box to the basal ganglia
>> region, where an alternate GM/WM threshold is used.
>>
>> other/CSF thresh = 10 (I think)
>> CSF/GM threshold = 70
>> GM/WM threshold = 190
>> GM/WM threshold = 197 (within 'basal_box')
>>
>> I do not see an option for 'b2 convert class-image to discrete'
>> which would allow one to choose alternate thresholds.
>>
>>
>> b2 load talairach-box /opt/brains2/bin/talairach/basal_box
>> Object loaded with filter: brains1
>> b2 convert talairach-box to mask talbox1 talpar1 expand= no
>> b2 convert class-image to discrete i1 mask= m1
>> Diagnostic Message: Thresholds 70 190 197
>>
>>
>> Usage   b2 convert class-image to discrete  <imageID> <mask= mask>
>>
>> Description     Converts a continuous tissue classified image into a
>>        discrete tissue classified image. The resulting image
>>        contains tissue codes from 0-9 (blood, other, etc),
>>        10 (CSF), 130 (GM), 250 (WM). The mask defines the
>>        subcortical region where the alternate threshold
>>        between GM and WM should be applied. If no mask is
>>        specified then 190 is used for the entire image.
>>
>> <imageID>       An identifier for an image
>>
>> <mask= mask>    The mask used to define the subcortical region.
>>
>>
>> Christoph Christmann wrote:
>>
>>> Hi all,
>>> during the segmentation process BRAINS2 not only provides a 
>>> _05_segm.img but moreover a discrete_*.img the latter representating 
>>> a real discrete image with classes for WM (white) and GM (grey). We 
>>> are not sure how this image was created and how to interpret it.
>>> The User's Guide states that it is possible to manually transform a 
>>> segmented image to a discrete image. However, we dont know which 
>>> parameters were used to do this automatically.
>>> Moreover we would like to know if anyone uses the discrete images in 
>>> the manual segmentation process in order to improve the reliability 
>>> or even the validity. Is there a rule of thumb for the paramters 
>>> (class image 2 descrete)?
>>> TIA
>>> christoph
>>>
>>>
>