BrainVISA

Have a look at the RIC toolbox developed by P. Kochunov and collegues, they may have this feature

We will switch to the 2010 pipeline in january Josselin,
hope everything will be overcome...

By the way, if you prefer removing the tumor, you can do it yourself. For instance remove it in the input MR scan.

BrainVISA pipeline is dedicated to T1. The resulting mask
is reported to other modalities using registration.
I think FSL deals with whatever modality.

If you click on the T1 bias correction in the pipeline, the last parameter
is delete_last_n_slices. This will be propagated to the rest of the pipeline.
I think the way you did it is OK, except bias correction
and histogram analysis did not enjoy getting rid of the bad slices.

Basically, if the brain mask looks OK, I do not think you will get additional information visualizing the histogram analysis. To be honest this is mainly dedicated to wizards... The good news is that the next release will include a more robust version of this analysis that shall overcome most of the...

At the very beginning of the bias correction process, there is a parameter used to exclude the N last slices of your image. It is especially useful when dealing with sagittal or coronal acquisition covering the head till the neck. The lowest part of the head indeed adds a lot of unusual intensities ...

I confirm the fact that we are finally working on robustness of the first part of the pipeline,
but i will take some time. Regarding your freezing stuff, the solution is usually
to change the undersampling parameter used by the VipHistoAnalysis command (-u flag).

It is not clear to me what you target, deep white matter? Because 5 mm below in the gyri would drive you into a mess? If you target deep white matter, a 5mm Morphological Opening applied on a mask of white matter should give you the object to be meshes. Not sure it would be spherical, except if you ...

Sometime, the topological trick to get nice rendering with open folds fails. You can force it removing the folds from the data directly using this set of commands: I will try to put the option somewhere in the next releases... VipSingleThreshold -i Lskeleton_subject.nii -t 19 -c b -o Lskel.nii VipSi...

Basically, there is two key tricks to be known for overcoming usual failures of the current pipeline: 1) When the histogram analysis fails, whatever how, try one by on the values of the menu dedicing for the histogram sampling (2, 4, 8...). Most of the time, one will work. 2) When the split procedur...

But I think that the problem comes from the histogram : the next step seems to be curious... I can not show the histogram (only the values, when I click on the pen). Is it normal? yes the pen is used for manual correction (you can guess the stats using the profile window of anatomist for instance) A...

Grey/CSF segmentation does not play any role. The old method based on perceptrons is based on stochastic minimization. Usually we trigger it a couple of time and keep the best result (very long stuff of course). There is a procedure for that in brainVISA called parallel recognition I think. This is ...

If there is a mean to formalize something through a grant, I am ready to spend some time with it.
It would simplify a lot of things...

It is not clear to me what problem you are talking about. If you have skull striped images, and robust grey/white matter segmentation coming from another software, I suggest to inject the brain mask at the right place (or even the hemisphere/cerebellum split). The grey/white matter mask however shou...