Search found 336 matches

by Jean-Francois Mangin
Thu Feb 05, 2009 10:26 am
Forum: BrainVISA
Topic: importing a mnc file: is there a database format?
Replies: 12
Views: 10118

Re: importing a mnc file: is there a database format?

It seems your specification of AC PC to go to Talairach is not working. Then the sulcus recognition is doing whatever, and a part of the brain is not labelled because too far from the normal places. As I said somewhere above, there is a brainVISA process creating a volume of sulcus labelled, it is i...
by Jean-Francois Mangin
Mon Feb 02, 2009 11:32 pm
Forum: BrainVISA
Topic: Anisotropic voxels
Replies: 14
Views: 9556

Re: Anisotropic voxels

Well, I processed your data on my laptop, with linux and distrib brainvisa 3.01 (quite old I am afraid...). Everything went fine. It is not a proof that another distrib is not buggy, but sincerely, I do not think anything like that should happen... An attempt of explanation: at the beginning, I coul...
by Jean-Francois Mangin
Sat Jan 31, 2009 9:25 pm
Forum: BrainVISA
Topic: Anisotropic voxels
Replies: 14
Views: 9556

Re: Anisotropic voxels

Well, I did this code myself, if it is doing such a resampling, it means
I am in the MCI state. Except if it is done inside brainVISA,not inth C level.
Can you post your image somewhere?
by Jean-Francois Mangin
Fri Jan 30, 2009 3:29 pm
Forum: BrainVISA
Topic: Anisotropic voxels
Replies: 14
Views: 9556

Re: Anisotropic voxels

To my Knowledge, brainVISA importation do not perform any resampling, and Anatomist should deal with your anisotropy
correctly. It is rather usual. Could you localiza the change of voxel size? Was it at importation?
by Jean-Francois Mangin
Wed Jan 28, 2009 9:02 pm
Forum: Anatomist
Topic: Convert .mesh file to text file?
Replies: 4
Views: 6726

Re: Convert .mesh file to text file?

The only thing I can tell you is that in BrainVISA, you can find a process calling SPM to convert affine normalization to our transformation format. So if you normalize your data with SPM and get an Anatomist transformation, you can use Aims commands to normalize the mesh. This is the end of my know...
by Jean-Francois Mangin
Tue Jan 27, 2009 10:38 pm
Forum: Anatomist
Topic: Convert .mesh file to text file?
Replies: 4
Views: 6726

Re: Convert .mesh file to text file?

Yes BrainVISA is distributed with hundred of commandlines including a FileConverter that can provide you with an ASCII mesh format and various other things. The way to run the command depends on the system linux/window/mac but is very simple. Everything is explained in the explanation about BrainVIS...
by Jean-Francois Mangin
Tue Jan 27, 2009 10:30 pm
Forum: AIMS
Topic: AimsImageSmoothing
Replies: 3
Views: 13821

Re: AimsImageSmoothing

Not so strange, if you resample an image with a cubic spline you get worse...
by Jean-Francois Mangin
Mon Jan 26, 2009 1:15 pm
Forum: AIMS
Topic: AimsImageSmoothing
Replies: 3
Views: 13821

Re: AimsImageSmoothing

I do not thing anything goes wrong. As far as I am aware, this command is based on the recursive implementation of R. Deriche, which is a very efficient way to approximate Gaussian smoothing. Hence getting this +/- epsilon in some places is possible if you smooth a binary image. If it is a pb for yo...
by Jean-Francois Mangin
Fri Jan 23, 2009 3:58 pm
Forum: BrainVISA
Topic: buckets at junction with brain hull
Replies: 3
Views: 3624

Re: buckets at junction with brain hull

These buckets are in the graph relations with the hull
by Jean-Francois Mangin
Wed Jan 21, 2009 2:19 pm
Forum: BrainVISA
Topic: importing a mnc file: is there a database format?
Replies: 12
Views: 10118

Re: importing a mnc file: is there a database format?

The main sulcus viewer is in the main features of brainVISA html page: It is called "Anatomist Show Fold Graph". Use the search facility if you are lost. And even simpler, the brainvisa processes generating the labelled sulcus has the viewer plug there, you trigger it clicking on the eye. ...
by Jean-Francois Mangin
Thu Jan 08, 2009 3:20 pm
Forum: BrainVISA
Topic: surface reconstruction
Replies: 15
Views: 13701

Re: surface reconstruction

Well,you should not generalize to fast...
How many data do you want to process?
Maybe you can come here with a few of them, let us say 5,
the BET segmentation, and we will play around...
Send me an E-mail on my address jfmanginATcea.fr,
you will make an appointment
by Jean-Francois Mangin
Wed Jan 07, 2009 10:39 am
Forum: BrainVISA
Topic: surface reconstruction
Replies: 15
Views: 13701

Re: surface reconstruction

The skull removed brain should be turned into a mask and replace the brain_mask generated by brainvisa.
You work in Paris? Yes you could visit us.
by Jean-Francois Mangin
Wed Jan 07, 2009 10:38 am
Forum: BrainVISA
Topic: How to handle lots of data in batch mode?
Replies: 24
Views: 26190

Re: How to handle lots of data in batch mode?

The process computing morphometric measurements is a bit special, you can select has many subject as you want to get only one file per sulcus. Otherwise, for the sulcus recognition, you use the iteration process selecting as many subject as you want. For the distribution of a lot of processing to a ...
by Jean-Francois Mangin
Sun Jan 04, 2009 10:52 pm
Forum: BrainVISA
Topic: surface reconstruction
Replies: 15
Views: 13701

Re: surface reconstruction

Peter Kochunov usually applies FSL to get the brain mask, for humans and monkeys (maybe you can get information on his web page). I never used FSL myself, I have no feeling about the behaviour of BET. The story is not just to get a brain mask. And I do not think it is the brain mask extraction that ...
by Jean-Francois Mangin
Mon Dec 22, 2008 1:11 pm
Forum: BrainVISA
Topic: What is the difference?
Replies: 7
Views: 6761

Re: What is the difference?

which error?