Search found 44 matches

by guillaume
Wed Aug 01, 2018 3:46 pm
Forum: Anatomist
Topic: save an image of the colormap like a colorbar in matlab/matplotlib
Replies: 1
Views: 1865

save an image of the colormap like a colorbar in matlab/matplotlib

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...
by guillaume
Thu Jul 12, 2018 2:24 pm
Forum: Anatomist
Topic: RGBA palette in pyanatomist
Replies: 6
Views: 2536

Re: RGBA palette in pyanatomist

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...
by guillaume
Mon Jul 09, 2018 3:01 pm
Forum: Anatomist
Topic: RGBA palette in pyanatomist
Replies: 6
Views: 2536

Re: RGBA palette in pyanatomist

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 ...
by guillaume
Fri Jun 08, 2018 1:37 pm
Forum: Anatomist
Topic: RGBA palette in pyanatomist
Replies: 6
Views: 2536

Re: RGBA palette in pyanatomist

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...
by guillaume
Fri Jun 08, 2018 10:44 am
Forum: Anatomist
Topic: RGBA palette in pyanatomist
Replies: 6
Views: 2536

RGBA palette in pyanatomist

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...
by guillaume
Tue Jan 16, 2018 11:45 am
Forum: BrainVISA
Topic: morphologist -> morphometry -> brain volumes error with data imported from freesurfer
Replies: 2
Views: 1874

morphologist -> morphometry -> brain volumes error with data imported from freesurfer

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:/...
by guillaume
Wed Mar 27, 2013 10:20 am
Forum: BrainVISA
Topic: datamind in brainvisa 4.3
Replies: 8
Views: 3908

Re: datamind in brainvisa 4.3

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...
by guillaume
Sat Mar 23, 2013 1:28 pm
Forum: BrainVISA
Topic: datamind in brainvisa 4.3
Replies: 8
Views: 3908

Re: datamind in brainvisa 4.3

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...
by guillaume
Fri Mar 22, 2013 6:53 pm
Forum: BrainVISA
Topic: datamind in brainvisa 4.3
Replies: 8
Views: 3908

Re: datamind in brainvisa 4.3

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...
by guillaume
Fri Mar 22, 2013 2:42 pm
Forum: BrainVISA
Topic: datamind in brainvisa 4.3
Replies: 8
Views: 3908

Re: datamind in brainvisa 4.3

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
by guillaume
Wed Mar 20, 2013 11:42 am
Forum: BrainVISA
Topic: datamind in brainvisa 4.3
Replies: 8
Views: 3908

datamind in brainvisa 4.3

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...
by guillaume
Tue Sep 18, 2012 4:21 pm
Forum: BrainVISA
Topic: morphomerty statistics and hierarchy
Replies: 3
Views: 1887

Re: morphomerty statistics and hierarchy

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...
by guillaume
Tue Sep 18, 2012 2:24 pm
Forum: BrainVISA
Topic: morphomerty statistics and hierarchy
Replies: 3
Views: 1887

morphomerty statistics and hierarchy

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_...
by guillaume
Thu Sep 13, 2012 2:11 pm
Forum: Anatomist
Topic: graph display properties
Replies: 6
Views: 4957

Re: graph display properties

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...
by guillaume
Thu Sep 13, 2012 11:10 am
Forum: Anatomist
Topic: graph display properties
Replies: 6
Views: 4957

graph display properties

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...

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