BrainVISA

Well I did not though you would use "split" literally... But I agree it is not always easy to search a forum. In fact I do not know enough about the way you use brainVISA to give useful advise. Most of the time, the pb stem from a bad bias correction, or from the fact that the cerebellum i...

Segmentation fault is not rare with this stuff, it was messed up a few years ago while working on monkey histological data. Never took the time to clean it up. Send me the histogram for my archives... A few tricks to solve your problem: 1) set a higher threshold on the minimum scale for the tracking...

Yes,
this topic has been answered a number of time in the forum. This procedure is not very stable...
Do a search on split.

Yann is right, it would be easy but would often lead to a low tech rendering. A lot of the tuning of the pipeline focus on the cortex, which is often leading to a bad mask of th cerebellum. The main reason is that the morphology of the cerebellul would require half a mm resolution to get reliable se...

Once again Arnaud should know which parameter wasa used, I try to get in touch with him.

You can use these images if you like, but I would prefer you to reference the papers:-)
Bias Correction: Mangin et al., MMBIA 2000
Brain segmentation, Mangin et al., MICCAI 1998
You can find complete references and pdf on http://lnao.fr

Thanks Denis...

Well, I am afraid the template used to guide the splitting procedure does not deal correctly
with sagittal images if you do not allow the importation to reformat the data into axial.

This command just applies RX+T to your image, X being the point coordinates from the first corner
of the image. Therefore, your rotation is just pushing your data out of the field of view.
You need to add a rotation (I know this format for the matrix is painful...).

Sorry Joost, we forget about you, Arnaud had to fight for survival during the last months...

You can find some snapshots with glossary on brainvisa site.

Arnaud has done one in the old time, I do not remember where it is hiden and if it is still OK... Your orientation issue is related to the fact that Anatomist leaves for historical reason in a mirror of the world, you need to flip one coordinate to have a real object. But you have to think a little ...

SO did you check the bias correction step (click on the eye in front of nobias). By the way, I was a bit surprise by your snapshot, does your image name includes a space? If you do not understand anything, put your data somewhere on the web and send me an e-mail, I will try to have a look when and I...

I forget to say that because of the weakness of the current recognition process, that can easily get trapped in a wrong solution, we usually use the process called parallel recognition: we do 3 recognition and keep the one providing the lowest energy. It is improving the situation but the time expen...

Congratulation, you went quite far without much help. Do not worry for the questions, it is a pleasure to get in touch with users like you. And we are sorry if the quality of the package has not reach yet a professional level... The folding patterns hide a lot of misteries. First, with the current s...