BrainVISA

Hello, until now I used to take a caption of the screen with the anatomist colormap window open and then manually crop the screenshot before I can incorporate it in my figure, which is not convenient. is there a way to save on the disk an image of the colormap automatically using pyAnatomist? thks f...

Yessssssssss it finally works! I used the texture_index, and also fixed one mistake: I was using object=fus which is not correct and should be replaced by objects=[fus]. So at the end, the following works fine: customPalette=a.createPalette("maPalette") customPalette.setColors(colors=color...

Hi Denis, almost everything works. The only remaining difficulty is with texturing mode. I tried with TexturingParams without success. I manage to do it manually (through the Anatomist GUI) by setting the 'mapping mode' in the 'fusion 2D control' panel of the fused object to 'Linear / A if B is not ...

Maybe I found the solution, but please confirm: in http://brainvisa.info/anatomist-4.6/dev_doc/commands.html I see the color_mode parameter that can be set to "RGB" or "RGBA" I tried to set in my code: colors = [] colors.extend([128,128,0,0]) colors.extend([128,128,0,255]) custom...

Hello, I would like to build a custom palette in pyanatomist that would include a transparency component (RGBA). I have been playing with RGB palette following the nice tutorial http://brainvisa.info/pyanatomist/sphinx/pyanatomist_tutorial.html, but I do not find examples for RGBA, is there any tuto...

Hi, I would like to compute brain volumes on data that were imported from freesurfer. I get the following error, meaning that the voronoi volume is locked, which is systematically the case when importing data from freesurfer. ---------------------------------------------- in CSF Classif 1 The file:/...

Hi Denis, I've never been so close... ... but it still doesnt work. Now I'm facing issues in the install of R packages so maybe shoul I contact Edouard... I've installed the precompiled version of R from the ftp, such that the gui of datamind appears properly however, at the start of datamind I have...

Denis, in fact I think the "i" was a mistake I personally made, it is not there in another install of bv4.3.0 I have on my laptop, sorry for that. Thank you for the link to the modules for R, I already have it from an old post on the forum and I'm currently trying to install them all. I've...

Good Denis, then I had to modify <brainvisa>/python/datamind/gui/MainGui.py like following: from datamind.config import MAJOR_QT_VERSIONi ==> from datamind.config import MAJOR_QT_VERSION i.e. just suppress the 'i' and now I have an error that corresponds to a library for R which is missing, but this...

Hi Denis,

in fact the problem seems to be the import of datamind.config.
In the IPyhton shell I can import datamind but not datamind.config, does it make sense for you?

gui

Hello, I see that the datamind toolbox is "available" by default in the stable version of brainvisa4.3... ...but have the following error when trying to launch it: Traceback (most recent call last): File "/home/me/BVs/brainvisa-4.3.0/bin/real-bin/datamind", line 70, in <module> i...

Thank you Denis, this selection GUI is a great tool I didn't tried before! However, I do not understand waht you mean by "use for instance "S.F.sup._right", even if it actually contains the whole lobe". For my first use I did select all sulcal names in the temporal lobe and get t...

Hi there, I would like to extract the morphometry stats from a graph of sulci at a level in the hierarchy that is different from the default setting. I mean for instance obtaining the descriptor 'surface' not for --S.F.inf._right, S.F.inter._right, S.F.sup._right, etc-- but instead for --PREFRONTAL_...

Hi Denis, one more time thank you for your fast answer! As you said, siCsvMapGraph.py seems doing the job I want. I tried it with a *_proba.csv resulting from the SPAM recognition and it works fine. However, I have one more question concerning the csv input: I see that the *_proba.csv looks like: no...

Hello, is it possible to add a new property to display onto a graph (graph display properties in anatomist)? I would like to visualize e.g. the posterior probabilities from the SPAM recognition process or a p-value that I would have computed for each sulcal piece. It seems to me that there should be...