BrainVISA

Hi, The hemispheres separation program failed. This is generally a consequence of an imperfect bias correction (or of incorrect AC/PC settings in PrepareSubject). Have you tried setting the "bias_type" parameter to "high Z bias" ? Denis The Split brain procedure found the hemisp...

Denis There is a gyral parcellation module in brainvisa (a part of Arnaud Cachia's PhD work). You can try it but it's still a bit experimental so you must be in "expert" user mode to access it: it is in "surface based analysis/white matter parcellation". It is based on the cortic...

Well, I have no guess for the moment. A few questions: did you manage to process some other datasets? (for instance the example in the distribution) did you spatially normalize your data before importation? are you sure your normalized data is not in a floating point format (I am not sure our import...

OK, I get your data and did some experiments: first data set (SENSE): While you use inversion/recovery sequence, your grey/white contrast is not very good, which is at the origin of your difficulties. If you can not improve your contrast, select the low contrast option at the top of the pipeline int...

Just a couple of information.
Olivier Coliot did a great job during the last weeks.
Thanks to him and Denis, Anatomist and BrainVISA
should be able to read Minc-1 format in the next release.
Jeff

Sorry,
the development of connectivity maps is in progress in our lab,
but is not yet in the current release. You will have to be patient.
The diffusion package should be improved a lot
during the next years. Furthermore, other teams may
add some features one day or another.
Jeff

In fact, the histogram analysis used in brainVISA is supposed
to switch automatically towards a specific procedure when
an inversion recovery sequence is detected. I will check
that this process behaves correctly with your data as soon
as I will be back from Canada.
Jeff

Well,
you triggered some very low level problem. I am afraid nobody except me can provide a diagnostic for that, and I do not have any clue
I am afraid you will have to wait for me to have a look at your data.
Sorry
Jeff

You can use this address:

Jean-Francois Mangin
Service Hospitalier Frédéric Joliot
Département de Recherche Médicale
Commissariat à l'Énergie Atomique
4, place du Général Leclerc
91401 Orsay Cedex, France

Yes, the sense reconstruction process may be the source of problem. I have never played with such anatomical data before. Can you put a few data on some ftp site or give us a CDrom with it? Unfortunately, I will be in Canada between the 20thmay and the 6th june, so you can take your time for that, I...

If you want an example simpler than the sulci, there is a hierarchy somewhere for deep nuclei, and a couple of brains with the nucleus-based graphs. Maybe we even gave them to Eric one day... You may visit us one of these days to see some demo about the graph-based capacities of Anatomist. In my opi...

Up to now, as far as I know, usual meshes do not have a stored color. If the set of meshes you generate is the same for each subject, the way to give them a color is to organize them into a graph, and use their name to get automatically a color from a model of your nomenclature described in a hierar...

I will be in Montreal the first week of june.
If it is not done at that point, I may try to discuss
about that with you. Anyway, we could have a beer together
arounf that time:-)
Jeff
PS I will send you VipMinc... sources tomorrow.

I am afraid this brainVISA's treatment is not really operational yet. It is tuned to SHFJ local PET acquisition features. Anyway, in general, for any registration problem, you may try first the AimsMIRegister Command, based on maximization of mutual information. BrainVISA registration toolbox should...

Christophe Grova said: j ai qques problemes pour convertir en GIS des cartes T IRMf qui sont en MINC .... en effet l outil que tu m avais file , que j ai un peu modifie pour mes besoin (qques Flips !) ... ne sort que des donnees en 16 bits or la il faudrait que je sorte du flottant ... d ou deux que...