| Re: Automatic Brain Detection from MRI scans [message #20529] |
Sat, 08 July 2000 00:00 |
Ivan Zimine
Messages: 40
Registered: February 1999
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Member |
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anne martel wrote:
>
> There is a lot of literature on how to segment brains in MRI scans
> ranging from fairly simple techniques which could easily be written in
> idl to very complex methods that would take months of work to implement.
> The best method to use will depend on the type of MRI scan you are
> working on and how accurate you want the segmentation to be. For large 3d
> volumes with > 50 slices then a method to set upper and lower threshold
> levels combined with 3d morphology operators to break the connections
> between the brain and the surrounding structures is the simplest
> approach.
> For scans with just a few slices a manual approach which allows
> thresholds to be set interactively and also allows the user to restrict
> the region from growing out into unwanted regions would work.
>
> This bit of code works for a single 128x128 T1 weighted slice (summed
> image)- values of r and thresh have been optimised for our images and can
> be adjusted. We use it to segment the brain from single slice dynamic
> sequences.
>
> mask = bytarr(s[1],s[2])
> r=7
> disc = SHIFT(DIST(2*r+1), r, r) LE r
> thresh=0.25*max(summed_image)
> mask=summed_image gt thresh
> mask=morph_open(mask,disc)
> ; now fill holes
> roi = search2d(mask,0,0,0,0) ;fill holes
> mask(*)=1
> mask(roi)=0
>
> Anne Martel,
> Dept Medical Physics,
> QMC, Nottingham
> anne.martel@nottingham.ac.ukqqq
>
> Michael Cugley wrote:
>
>> I've just been given an assignment involving MRI scans of the brain;
>> one of the "wish list" features is being able to automatically detect
>> the brain within each scan. Failing that, some way of making the
>> process easier, such as a single click on "brain", and the program
>> then selecting the rest of the "brain" from there (similar to "magic
>> wand" selection tools in paint programs).
>>
>> Has anyone any experience in this area? References to look up? I'd
>> rather not have to re-invent the wheel on this one...
>>
>> --
>> Michael Cugley (mjcugley@medphys.dundee.ac.uk)
also regs=label_region(mask) & histogram(regs) can help to get rid of
non-brain structures
and roberts function to get the contour of the cortex.
--
Ivan Zimine | ivan.zimine@physics.unige.ch
Dpt. of Radiology | (+41 22) 372 70 70
Geneva University Hospitals |
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| Re: Automatic Brain Detection from MRI scans [message #20548 is a reply to message #20529] |
Fri, 07 July 2000 00:00  |
anne
Messages: 9
Registered: February 2000
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Junior Member |
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There is a lot of literature on how to segment brains in MRI scans
ranging from fairly simple techniques which could easily be written in
idl to very complex methods that would take months of work to implement.
The best method to use will depend on the type of MRI scan you are
working on and how accurate you want the segmentation to be. For large 3d
volumes with > 50 slices then a method to set upper and lower threshold
levels combined with 3d morphology operators to break the connections
between the brain and the surrounding structures is the simplest
approach.
For scans with just a few slices a manual approach which allows
thresholds to be set interactively and also allows the user to restrict
the region from growing out into unwanted regions would work.
This bit of code works for a single 128x128 T1 weighted slice (summed
image)- values of r and thresh have been optimised for our images and can
be adjusted. We use it to segment the brain from single slice dynamic
sequences.
mask = bytarr(s[1],s[2])
r=7
disc = SHIFT(DIST(2*r+1), r, r) LE r
thresh=0.25*max(summed_image)
mask=summed_image gt thresh
mask=morph_open(mask,disc)
; now fill holes
roi = search2d(mask,0,0,0,0) ;fill holes
mask(*)=1
mask(roi)=0
Anne Martel,
Dept Medical Physics,
QMC, Nottingham
anne.martel@nottingham.ac.ukqqq
Michael Cugley wrote:
> I've just been given an assignment involving MRI scans of the brain;
> one of the "wish list" features is being able to automatically detect
> the brain within each scan. Failing that, some way of making the
> process easier, such as a single click on "brain", and the program
> then selecting the rest of the "brain" from there (similar to "magic
> wand" selection tools in paint programs).
>
> Has anyone any experience in this area? References to look up? I'd
> rather not have to re-invent the wheel on this one...
>
> --
> Michael Cugley (mjcugley@medphys.dundee.ac.uk)
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| Re: Automatic Brain Detection from MRI scans [message #20568 is a reply to message #20548] |
Tue, 04 July 2000 00:00 |
David Fenyes
Messages: 10
Registered: November 1996
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Junior Member |
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>>>> > "Michael" == Michael Cugley <mjcugley@tigger.medschool.dundee.ac.uk> writes:
Michael> I've just been given an assignment involving MRI scans of
Michael> the brain; one of the "wish list" features is being able
Michael> to automatically detect the brain within each scan.
One of my ex-colleagues as a grad student developed a heuristic
algorithm that seemed to be quite effective, which he used as part of
his thesis research:
Bedell, B.J., Narayana, P.A.: Automatic removal of extrameningeal
tissues from MR images of human brain. J. Magn. Reson. Imag. 6:939-943, 1996.
Bedell, B.J., Narayana, P.A., and Johnston, D.A.: Three-Dimensional
image registration for human brain. Magn. Reson. Med., 35:384-390, 1996.
David.
--
David Fenyes -- _dave_@_fenyes_._net_ -- remove the '_'s for address
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