BrainVISA

Sorry,
I get this message a couple of times during the last weeks. Maybe something get broken in the last release,
but I did not have time to investigate. Maybe you can send me the histogram by Email (the *.his file
generated by thehistogram analysis).

I tend to follow Denis, it could stem from noise in the grey white classification in some of the sulci. This noise would disturb the depth estimation driving the split of simple surfaces into pieces according to putative pli de passage (depth minima)... By the way, there is an option of the commandl...

They are correct, just over segmented?

sometimes, after typing something in this interface, I noticed you have to wait a few seconds for brainVISA to update
everything correctly. I was distubed a bit like you.

Try to change histogram bining with "-u" option. Normally it is chosen automatically, but with some data this is buggy. You can see in the log window what is the value chosen automatically. Then taking this value to begin your search, test another one. For instance if the undersampling is ...

In fact there is often a misunderstanding about BrainVISA. The section you are talking about is providing an abstract to be cited if you want to talk about brainVISA as a framework. BrainVISA is what is sometimes called a glue software. It is hosting various toolboxes. So you should often rather cit...

For the crop: Aims/VipSubVolume -h I do not know what you can do with the Nifti format. I guess you can play with origins but I do not know how. Temporarily you can create an Anatomist transformation file Tx Ty Tz 1. 0. 0. 0. 1. 0. 0. 0. 1. Give two different referentials to the initial volume and c...

Denis did that stuff, I do not know which flip he tooked into account, but I guess this one should. But it is not even clear to me which rule is given to choose the point of the interhemispheric plane. At the time I was dealing with that, this point could be anywhere. Is he supposed to be at the top...

You mean antenatal imaging? We are working on that for years, but it is not ready to
distributed. You will get in a lot of trouble with a standard acquisition because of slice thickness.

What process do you use to create the surface? Do not use the one called 5-something, unfortunatelly I never had time to finish it... YOu should use the one active in the complete pipeline. In case nothing works, you may have problem with bias correction. Let more freedom to the correction through l...

There is a safe way to protect your manual work. Somewhere in the toolbox, you can find some validation processes. If you run the one locking the splitBrain, it will never be modified by any other brainVISA process. I know it would be better to have a graphical feedback but we never found the time t...

I think something like that has already been developed by Pauline Roca and Denis Rivière to select fiber tracts from
a parcelation of the white matter surface. Maybe you should visit us one of these days...

Is it happening with only one dataset or a whole database?

No,
the segmentation process is imposing a spherical topology to the white matter surface.
This is at the origin of your problem, sometimes a thread of voxels is connected
in the final result. You can not remove it with simple connectivity analysis.
But tuning the segmentation parameters could work.

There is a surface cleaner somewhere here, but it is not distributed yet. I am afraid the only solution is to remove by hand the spurious chains of voxels at the origin of the problem. You can also try to tune the segmentation parameters (white matter/grey matter stats, or pressure inside white matt...