[Brains-users] Some questions regarding segmentation
Christoph Christmann
christma at zi-mannheim.de
Wed Jan 25 00:09:59 PST 2006
Dear Ronald, dear Eugene,
thanx a lot for the very detailed answers. I will definitely go all
the recommended steps and report
any problems that cannot be solved by your answers or the manual. Is
there a kind of periodical FAQ for the mailing list?
Best regards
Christoph
At Tuesday 24.01.2006 19:50, Ronald Pierson wrote:
>Okay, sounds like you are on the right track. The brain box is intended to
>be the size that you show, and there is a reason why. In our segmentation
>routine we let BRAINS pick plugs throughout the brain as a means of sampling
>the tissue types. We chose this set of boxes because we want to only pick
>those areas that we are 100% sure are brain. This is undersized, so we know
>that what is in here will be brain or CSF, not bone, fat, etc. That makes
>sure that the training classes used for classification are the tissues we
>want. Next, a set of discriminant functions are created to classify the
>image, based on those training sets. Then, the entire image is classified.
>
>Sounds like what you have done to generate the brain will do the job. The
>brain mask that we use is generated with an artificial neural network, that
>was trained on manually traced brains. The accessed through >workup >run
>neural >MR5/MR6 > Brain.
>
>We added a second segmentation step a few years ago. This takes the ANN
>brain mask, cleans it a bit with several routines, then reruns the
>segmentation using the brain mask as the region for picking plugs. This
>helps get a more representative set of tissue plugs and helps account for
>intensity fall-off in the posterior and inferior regions. This is invoked
>with the little button "bootstrap" on the last screen of the segmentation
>GUI.
>
>I would guess that if you use both the T1 and T2 for segmentation you should
>end up with a good image, but if you don't, here are a few suggestions:
>
>The T1 and T2 must be well registered. This is the cause of many problems
>in segmentation. Check spots on the arterior regions, placing the
>crosshairs at some clear borders on the T1 and T2 image. Toggle between the
>two (using the spacebar or the Selector) and make sure the borders are in
>the same place on both images. Also check the cerebellum.
>
>The other main problems with the segmentation routine itself are with the
>sampling of the tissues, or as we call it, plug picking. If you load the
>csf_plugs.mask, grey_plugs.mask and white_plugs.mask, you will see what has
>been picked. The main things that affect this are set in the first window
>of the BRAINS2 segmentation GUI. The ones I could suggest changing are
>permissiveness and trim mean outlier. Permissiveness refers to the first
>step in purifying the plugs (training classes). For each plug of 8 voxels
>the variance is found. If that is above a certain level, the plug is
>considered to NOT be pure tissue, and it is discarded. Permissiveness
>refers to how much variance we allow, the larger the number the more
>variance. If your images are speckly or poorly registered, you may need to
>increase it.
>
>After the purity of the plugs is tested, they are grouped by k-means
>clustering into the tissue classes. Next, the outliers are removed from
>each set of plugs (now called tissue training classes). Trim Mean Outlier
>(TMO) refers to how many SD from the mean (in each image type) at which the
>plugs are removed. If you remove too much (a TMO that is too low) there
>will be unclassified areas (black voxels) on the borders between CSF, Grey
>and white - it won't know what to do with partial-volumed voxels. If you
>remove too little (a TMO that is too high) you may end up with fuzzy,
>indistinct borders between the tissue types.
>
>So, I suggest
>1. Use both T1 and T2
>2. Check registration
>3. Look at the plugs and see if they really represent the tissues. If not,
>try changed in the permissiveness and the trim mean outlier.
>
>Long answers to a short question, but I think it is helpful if one looks at
>the process - you can sometimes pick up on why there are problems, though
>sometimes it is difficult.
>
>Feel free to email screen shots of your results, they are quite helpful to
>my understanding the problem.
>
>Ron
>
>
>-----Original Message-----
>From: brains-users-bounces at psychiatry.uiowa.edu
>[mailto:brains-users-bounces at psychiatry.uiowa.edu] On Behalf Of Christoph
>Christmann
>Sent: Tuesday, January 24, 2006 11:10 AM
>To: brains-users at psychiatry.uiowa.edu
>Subject: RE: [Brains-users] Some questions regarding segmentation
>
>Dear Ronald,
>
>Thanks a lot for your suggestions!
>
>We obtain only T1 and T2 data but at least this is mandatory for all
>of our anatomic data. So we easily can include T2 data, too. I wasnt
>quite sure if the data was used for the segmentation, too, even
>though I was able to specify the T2 data in the segmentation dialog.
>I used the T2 data for the blood vessel definiton, too. I'll go
>trough all steps in the manual again and try the segmentation without
>prior skull stripping.
>
>One question, however, remains: In the segmentation dialog there is a
>specification of a standard box (talairach) which is too small for
>all our brains (I couldnt figure out the reason for that - I append a
>picture). Alternatively I used a mask (concurrent option) that I
>created with a skull stripped image (by means of the image tools-
>threshold option). Is there an alternative algorithm? What could be
>wrong with the box?
>
>Thanks again!
>
>Sincerely
>
>Christoph
>
>
>At Tuesday 24.01.2006 15:29, Ronald Pierson wrote:
> >I suggest you take some time to go through the Standard Workup manual
> >that can be found on the WIKI page of our web site.
> >
> >http://www.psychiatry.uiowa.edu/wiki/index.php?title=BRAINS_GETTING_STAR
> >TED
> >
> >BRAINS does a full workup, including creation of a fantastic mask of the
> >brain. We don't call it skull stripping, it really is more focused on
> >careful definition of brain and CSF.
> >
> >Standard workup is normally done with a T1 and T2, with addition of a PD
> >if it is available. A T1-only classified image is really not the best,
> >no matter what package is used to create it.
> >
> >A quick summary of our workup -
> >
> >1. The first step is to realign the T1 (AC-PC), pick Talairach
> >parameters, then coregister the T2 to the T1 (using alignlinear or
> >mutual information coregistration from the toolbar).
> >
> >2. Then, blood is traced. Tissue classification (we also call this step
> >segmentation) is completed using both a T1 and T2 so that there is a
> >very clear definition of brain vs nonbrain. If you us only a T1-like
> >image, you will need to use a different designation for blood, maybe the
> >250 voxels from the top of the image (outside of the image space). That
> >is because blood is very similar in intensity to gray matter on a T1,
> >and you can't make any distinction to discriminate between blood and
> >gray matter without more information from the T2.
> >
> >3. At that point, and actually as part of tissue classification, a mask
> >is generated that is analogous to what you refer to as skull stripping.
> >We go the extra step to manually edit this brain mask before measuring
> >brain volumes. We really feel that this brain mask is far superior to
> >anything else currently available.
> >
> >FYI - we actually don't like the use of basal gray and basal white any
> >more. There really is too much variability between traces in what gets
> >picked.
> >
> >Ronald Pierson
> >
> >
> >-----Original Message-----
> >From: brains-users-bounces at psychiatry.uiowa.edu
> >[mailto:brains-users-bounces at psychiatry.uiowa.edu] On Behalf Of
> >Christoph Christmann
> >Sent: Tuesday, January 24, 2006 3:02 AM
> >To: brains-users at psychiatry.uiowa.edu
> >Subject: [Brains-users] Some questions regarding segmentation
> >
> >Hi all,
> >
> >At first I am facing a serious problem during the segmentation. I did
> >skullstrip, import, resample, crop and lighten up a FLASH image. Then
> >I created a mask of the brain (with image tools - threshold) the
> >Talairach parameters, and sampled ROIs for venous blood and basal
> >white and grey matter. Images, ROIs and masks show up in the
> >segmentation dialogs (i.e. no appearance of a '-1'). However, after
> >running segmentation (without BOOTSTRAP) the tissue qualification
> >seems shifted, for example white matter will completely be qualified
> >as grey matter. Has anyone an idea what's inducing this behaviour and
> >how this can be fixed?
> >
> >A second question is concerning the skull stripping. Is there any
> >tool apart from MRIcro that could be used effectivly to separate the
> >brain?
> >
> >The last question applies for the use of T2 images. While it seems
> >quite reasonable to integrate the T2 images for the ROI analysis I
> >wonder if the T2 image is used for the segmentation of the T1 image.
> >
> >Thanks in advance for any hint!
> >
> >Christoph
> >
> >
> >
> >
> >
> >--
> >Christoph Christmann christma at as200.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 Neuropsychology D-68159 Mannheim J5
> >and Clinical Psychology
> >
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>--
>Christoph Christmann christma at as200.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 Neuropsychology D-68159 Mannheim J5
>and Clinical Psychology
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Christoph Christmann christma at as200.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 Neuropsychology D-68159 Mannheim J5
and Clinical Psychology
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