Search found 336 matches

by Jean-Francois Mangin
Fri Jan 11, 2013 1:27 pm
Forum: BrainVISA
Topic: Exporting an entire sulci to matlab
Replies: 6
Views: 3992

Re: Exporting an entire sulci to matlab

No, you can not get point correspondence. This is a very complex issue because some sulci are interrupted in some subjects.
by Jean-Francois Mangin
Thu Sep 06, 2012 1:19 pm
Forum: BrainVISA
Topic: T1 bias correction error
Replies: 2
Views: 2320

Re: T1 bias correction error

Could we get it?
by Jean-Francois Mangin
Thu Jul 05, 2012 12:17 pm
Forum: BrainVISA
Topic: Morphologist with normalization FSL
Replies: 1
Views: 1862

Re: Morphologist with normalization FSL

A very pragmatic way would be to click on AC PC as usual for one brain, this will generate the file somethingIforget.APC in the folder of this subject. You can duplicate the file for all the other subjects. You just have to change the subject name in the file name. For the other subject you just ski...
by Jean-Francois Mangin
Mon May 14, 2012 12:50 pm
Forum: BrainVISA
Topic: Topology of cortical mesh
Replies: 4
Views: 2054

Re: Topology of cortical mesh

In fact the procedure to get the mesh has changed so there is an explanation.
I am surprised there was still a problem in the older version, but maybe it is
something that happened temporarily in the 2011 version because of a bug.
by Jean-Francois Mangin
Thu Sep 08, 2011 6:10 am
Forum: BrainVISA
Topic: Gyri parcellation for 3.1 graph version
Replies: 8
Views: 2961

Re: Gyri parcellation for 3.1 graph version

Are you sure some nodes are not labelled? It could be that the triangles linking nodes with different labels are white?
by Jean-Francois Mangin
Fri Aug 26, 2011 10:52 am
Forum: BrainVISA
Topic: advice for Morphologist on Inversion Recovery images?
Replies: 1
Views: 1539

Re: advice for Morphologist on Inversion Recovery images?

What can of sequence is it? Inversion recovery is the most usual sequence we use and it is not what we get... Anyway, everything should go fine with something as incredible, the brain is already segmented... I assume Morphologist did not work for you to post this question? Can you send a dataset to ...
by Jean-Francois Mangin
Fri Aug 26, 2011 10:44 am
Forum: BrainVISA
Topic: BrainVisa Talairach
Replies: 7
Views: 2853

Re: BrainVisa Talairach

Yes your problem is that our Talairach system puts CA at the origine I guess, leading to negative coordinates for the left of the volume, which can not be handled by our resampling command. The solution is to add a translation as you did. Otherwise, if you open the transformation window of Anatomist...
by Jean-Francois Mangin
Tue Jul 19, 2011 2:59 pm
Forum: BrainVISA
Topic: brainvisa parameter change
Replies: 1
Views: 1313

Re: brainvisa parameter change

Honestly, this issue could deserve some experiment, but I do not think the sulcus depth would be changed by this parameter. This pression was mainly introduced to slightly improve the grey/white matter interface, which is far to be the strongest point in Morphologist because it is only a byproduct o...
by Jean-Francois Mangin
Thu Mar 10, 2011 2:10 pm
Forum: BrainVISA
Topic: English nomenclature
Replies: 3
Views: 3131

Re: English nomenclature

I am afraid you have to make up your mind yourself about these disagreements. The point is that very few people really worked on this topic, and each of them used unclear definitions. The fact that we based our point of view on the sulcal root theory of Jean Regis led us to develop a specific nomenc...
by Jean-Francois Mangin
Fri Feb 18, 2011 9:48 am
Forum: BrainVISA
Topic: Field regularisation low contrast
Replies: 5
Views: 2943

Re: Field regularisation low contrast

Is the brain mask OK?
IS the histogram analysis OK (I mean you can check easily the mean value for grey and white matter,
to see if they fit the nobias image (use the profile window in Anatomist)
by Jean-Francois Mangin
Sun Feb 06, 2011 9:18 pm
Forum: BrainVISA
Topic: Field regularisation low contrast
Replies: 5
Views: 2943

Re: Field regularisation low contrast

If your data have a good contrast, it could be related to
a failure of histogram Analysis. Switch from auto to a couple
of other fixel values for the sampling.
by Jean-Francois Mangin
Sat Jan 29, 2011 10:26 am
Forum: BrainVISA
Topic: Segmentation pipeline
Replies: 2
Views: 1749

Re: Segmentation pipeline

Try to change the parameter tuning the histogram sampling

good luck

hope all this mess will disappear in the next release...
by Jean-Francois Mangin
Fri Jan 21, 2011 8:56 pm
Forum: BrainVISA
Topic: Problems segmenting MRI image from "MEGSIM"
Replies: 2
Views: 2283

Re: Problems segmenting MRI image from "MEGSIM"

Maybe the histogram analysis failed, you should try to modify one of the parameter
for histogram sampling.
by Jean-Francois Mangin
Fri Jan 21, 2011 8:53 pm
Forum: BrainVISA
Topic: projection of INSULA onto the white mesh
Replies: 2
Views: 1845

A

I guess you are right, because the INSULA is the bottom of the Sylvian Valley in a way. but it was 10 years ago, I will reanimate the spirit of Arnaud... Olivier should know more about that because of Cedric's work. But with Cedric I remember doing something else to get the pole while one of his tri...

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