BrainVISA

Hi Jane, 1. Yes, of course the results of automatic sulcal identification are not always very good. The idea of fixing some labels at the beginning is interesting, but unfortunately we haven't thought of it and so it's not possible now to prevent the system from changing the label of some nodes. We ...

No, 2.3.2 is just a bugfix release (or contains small improvements that don't affect the internal infrastructure). This feature requires the new infrastructure of the future version of Anatomist. But it's in the development packages, some of them are available on the download page, but are maybe not...

Hi Peter, This is a feature of the next version of Anatomist... In Anatomist 1.30 (the current stable version), textures are 1D or 2D (coords in a palette or in a 2D image). There is no direct RGB mode in textures in OpenGL as far as I know (unless I have missed something in the doc), so RGB texturi...

Hi Jane, What happens to you is... just normal ! Everything is working... The recognition process is long (approximately 2 hours of computing on a standard PC) and BrainVisa doesn't update the outputs of the command during this time. You can see where it is if you look at the log (type <ctrl>-L to o...

Well, I confirm your trouble is due to space characters in filenames. This is a bug in BrainVisa and in our other programs. I have fixed them all (I think) here and we will provide an update, ahem, very soon, yes, this time we will do it...

Denis

Oh I think I know what is going wrong ! I guess the command that builds the cortical folds graph doesn't like filenames containing space characters... Here is one of the few examples of C commands (Vip commands) running other commands (Aims C++ commands) and these old programs are not protected agai...

Well,
I have to test the whole pipeline on Windows, I haven't tried it for a while. I don't have a Windows machine right now so I will make the test in a few days. Please be patient (or use the Linux version during the while)...
Denis

The error message about DcmDataDictionary is a known problem in the dicom library that we have solved here for the next release. But I thought it doesn't prevent images from being actually read, but just some info from the Dicom header will be missing. Can Anatomist load the image or not ? Anyway th...

Hi Manik, We do use such data in a "shared" database provided with BrainVisa. We have stored there the hemisphere separation template, standard transformation matrixes (SPM<->our Talairach system), anatomist hierarchies, recognition models, etc. This database is located in the "share&...

I thought Anatomist transmitted the coordinates in the referential of the window. If it always could, it would certainly be better, but here it's not possible: BV asks Anatomist for the coordinates of the last click when it needs them, and we don't know which window was involved (the window the use...

I think I know what happens. First, once an image is assigned a transformation to a "standard" referential (our Talairach system or SPM normalization system), it is always loaded by BrainVisa with this transformation into Anatomist. This means that coords taken from Anatomist by BV before ...

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

Yes, it makes sense to delimitate the gyral regions on the inflated brain and to measure them on the un-inflated one. The only problem is that, as I said, we have made no tool right now to measure the area of mesh inside a drawn region. It would be easy to do, but it's not done up to now... What I e...

The gyral parcellation tool automatically defines gyral regions delimited by the main sulci (there is a list of sulcus limits somewhere) and makes a "gyri graph" from them, which is quite similar to the sulci graphs (but for gyri). For more information, read about Arnaud Cachia's work: A. ...

1) Yes "Ana Inflate Cortical Surface" uses the white matter mesh. But measuring cortical areas on an inflated brain seems not a good idea to me because the inflation induces local deformations so areas are not preserved. 2) No we don't have yet a tool to calculate a cortical thickness map....