[Brains-users] brain mask - problems with automatic definition
Christoph Christmann
christoph.christmann at zi-mannheim.de
Mon Feb 19 23:28:18 PST 2007
This looks pretty different from our AC-PC lines, we will try it!
Since I noticed the high quality of your pictures in respect of GM-WM
contrast I have a further question regarding the measurements. Until
recently we were gathering all data on an old 1.5T machine. Since we
now have a new 3T device we think about setting up a new protocol.
What could you recommend regarding sequences and parameters? We
actually could obtain T1 (FLASH or MPRAGE), T2, PD and a dark fluid
sequence. Moreover, we wonder if it could be preferable to use an
anisotropy map from a DTI sequence instead of a PD.
Christoph
At Monday 19.02.2007 22:39, Ronald Pierson wrote:
>Here is what I think is pretty normal for our resampling. AC is picked just
>above the AC as it crosses the midline. This brain has the commisure going
>superiorly on the left side, but we just look at it on the midline.
>
>PC is one we argue about...I think the most anterior part is just a little
>"flip" of tissue that doesn't extend left or right. If you look carefully
>for the band of white matter that crosses the midline, I believe that most
>of the time you will find it just posterior to the flip. However, there is
>an atlas that shows it as centered in the "flip", and many people go by
>that. Bottom line, for most scans, the resolution makes it hard to see, so
>it is important to have a rule that is very consistently usable, regardless
>of image quality.
>
>As a quick visual check, I use the rule that the ACPC line, seen on the
>sagittal view, will have the corpus calosum resting on it anteriorly, and
>posteriorly it will just clip off a small piece of the occipital lobe.
>
>
> Ron
>
>
>-----Original Message-----
>From: Christoph Christmann [mailto:christoph.christmann at zi-mannheim.de]
>Sent: Monday, February 19, 2007 10:41 AM
>To: Ronald Pierson; eugene-zeien at uiowa.edu
>Cc: 'Brains-users at www.psychiatry.uiowa.edu'
>Subject: RE: [Brains-users] brain mask - problems with automatic definition
>
>Oops,
>
>this could hit the nail on the head: we are actually setting the AC
>line in the middle of the commisure while setting the PC line in the
>middle or even superior (since it is not alway quite clear where it
>ends in inferior direction). This is our appraoch coming from the
>Talaraich transformation of the BrainVoyager world, i.e. fMRI. So we
>will definitely test to set the AC and PC points according to your
>standards.
>
>Could you be so kind to provide us some significant pics, for example
>a sagittal and a related axial view of AC and PC in the usual
>Iowanian brains? ;)
>
>Second we would like to know if there was a way to train the net
>anyway since this we hope to still better the results. Correcting the
>brains mask is a very boring work for our students.
>
>Thanks a lot for your support
>
>Christoph
>
>
>
>
>At Monday 19.02.2007 17:31, Ronald Pierson wrote:
> >Just thought I'd chime in - wanted to earlier, but have been too busy.
> >
> >I think one of the main problems we run into is when the brain is in an
> >orientation that places part of the brain outside of where our probability
> >map says it should be. Take a look at the sagittal window on the
>attachment
> >that Eugene sent last week. Then, take a look at the midsagittal slice of
> >your typical scan. Now, I can't tell for sure from your snapshots, but it
> >would appear to me that your brain is tilted back a fair amount compared to
> >our standard, average orientation. Is that the case? If so, then the
> >superior frontal lobe will be higher than normal, and the cerebellum lower
> >than normal inside the Talairach bounds, pushing them outside of the
>regions
> >where the ANN expects to find the brain.
> >
> >Is this a consistent problem? If so, maybe you are picking the AC and PC
> >different from us. We pick the AC point to be just above the AC, and the
>PC
> >point just below it. If you picked both of them in their centers, the head
> >would be rotated back further than our "typical" orientation.
> >
> >We are currently developing new methods to remove the dependence on
> >Talairach bounds and to better handle the nonstandard brains and
> >orientations better. Hopefully in the next 6 months or so we will release
>a
> >method for a good no-trim brains on >90% of the cases.
> >
> >Ron Pierson
> >
> >
> >
> >-----Original Message-----
> >From: brains-users-bounces at psychiatry.uiowa.edu
> >[mailto:brains-users-bounces at psychiatry.uiowa.edu] On Behalf Of Eugene
>Zeien
> >Sent: Monday, February 19, 2007 10:17 AM
> >To: Christoph Christmann
> >Cc: Brains-users at www.psychiatry.uiowa.edu
> >Subject: Re: [Brains-users] brain mask - problems with automatic definition
> >
> >I have, in fact, had very similar problems. "standard workup"
> >is not a part of my daily routine, but I needed to generate a
> >brain mask for a project. Rather than ask a more experienced
> >person to create one, I decided "I can do this". Then I
> >proceeded to do just about everything wrong. :-) One by one,
> >I found the problems and fixed them. Eventually (about 1 day)
> >I had the neural net making pretty brains.
> >
> >The basic issue I see with your mask is:
> >The neural net is not finding the expected anatomical boundaries. So,
> >the end result is merely the probability
> >mask where more than 50% of the subjects used to train the
> >neural net had a region identified as brain.
> >
> >Why? Well, there can be several causes.
> > incorrect talairach bounds
> > over-inclusive blood traces which lead to
> > bad segmentation
> > incorrect image specified for the neural net's use
> >
> >There may be other ways to confuse the neural net, but these
> >are the things I had done. Of those problems, you've checked
> >three. The only one left is if the segmented image has CSF
> >classified as blood. So, load up the image, then
> > Viewers->Tracker
> >and set the crosshairs in brains2 to somewhere in the
> >ventricles. The values (poke around several places) should
> >be around 30. If you see the values showing up as 0 or 1, then
> >something has gone wrong in the segmentation. The values
> >outside the brain/head should be 0. You should only find 1's
> >where major blood vessels exist.
> >
> >On Mon, 2007-02-19 at 10:15 +0100, Christoph Christmann wrote:
> > > hi gene,
> > >
> > > we always used proper talairach bounds. here, we just added the image
> > > to some former work where we used the 'talairach box' lines for
> > > different orientation purposes.
> > >
> > > are there any further hints regarding the brain mask? dont you have
> > > similar problems?
> > >
> > > christoph
> > >
> > > At Friday 16.02.2007 16:52, you wrote:
> > > >Christoph,
> > > > Are the red lines on the images you sent the Talairach bounds?
> > > >If so, they are nowhere near the correct location. Try re-defining
> > > >the talairach boundaries, then run the neural net again.
> > > > I've attached a picture showing proper talairach boundaries.
> > > >The 2 points near the center are supposed to be the anterior and
> > > >posterior commissures.
> > > >gene
> > > >
> > > >On Fri, 2007-02-16 at 12:35 +0100, Christoph Christmann wrote:
> > > > > hi,
> > > > >
> > > > > the segmented image looks reasonable. I attach some pictures
> > > > > elucidating the actual situation. I am especially surprised that the
> > > > > cerebellum border is not found correctly although it seems to be
> > > > > obvious as you can see in the brain_mask_cor_seg.jpg file. You can
> > > > > see in the other two images, that T1 and T1 is realigned quite well
> > > > > (cost function < 0.45).
> > > > >
> > > > > If you would have any idea to use other programs to get the brain
> > > > > mask I would try this way, too. Actually, we started with BrainSuite
> > > > > but found it to be less precise, too - although in other regions.
> > > > > Maybe we end up with an SPM or FSL segmentation for the mask.
> > > > >
> > > > > Best regards
> > > > >
> > > > > Christoph
> > > >
> > > >
> > >
> >_______________________________________________
> >Brains-users mailing list
> >Brains-users at www.psychiatry.uiowa.edu
> >http://www.psychiatry.uiowa.edu/mailman/listinfo/brains-users
>
>--
>Christoph Christmann christoph.christmann at zi-mannheim.de
>Psychologist, MEE Fon/Fax +49 621 1703 63 18/05
>Central Institute of Mental Health http://www.zi-mannheim.de
>Department of Clinical D-68159 Mannheim J5
>and Cognitive Psychology
>
>
>
>
--
Christoph Christmann christoph.christmann at zi-mannheim.de
Psychologist, MEE Fon/Fax +49 621 1703 63 18/05
Central Institute of Mental Health http://www.zi-mannheim.de
Department of Clinical D-68159 Mannheim J5
and Cognitive Psychology
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