Search found 29 matches

by f4bry
Thu Nov 15, 2018 8:27 pm
Forum: BrainVISA
Topic: 'SelectByNomenclature' script
Replies: 3
Views: 13960

Re: 'SelectByNomenclature' script

Hi Denis,
Unfortunately this doesn't solve the issue. Since I am not getting error messages I don't know how to debug it.
Is there a method to check which objects are loaded in the Anatomist window?

Thank you!
f4b
by f4bry
Wed Nov 07, 2018 8:30 pm
Forum: BrainVISA
Topic: 'SelectByNomenclature' script
Replies: 3
Views: 13960

'SelectByNomenclature' script

Dear All, I am trying to reproduce the following example with brainvisa-4.6.1 on a mac osx 10.14. The graph is loaded in Anatomist but the 'PREFRONTAL_right' doesn't show up. import anatomist.direct.api as anatomist from soma import aims import os a = anatomist.Anatomist() sh = aims.carto.Paths.shfj...
by f4bry
Fri Dec 16, 2016 7:37 pm
Forum: BrainVISA
Topic: Sulci Curvature Stats
Replies: 2
Views: 7682

Re: Sulci Curvature Stats

Hi Denis,
Very clear, thank you so much!
Fab
by f4bry
Fri Dec 16, 2016 5:27 am
Forum: BrainVISA
Topic: Sulci Curvature Stats
Replies: 2
Views: 7682

Sulci Curvature Stats

Hi,
How 'Sulci Curvature Stats' tool computes the curvature? Is it the mean curvature over all the sulcal mesh vertices?
Thank you,
Fab
by f4bry
Wed Aug 10, 2016 2:30 am
Forum: BrainVISA
Topic: Sulcus Parametrization 2015 , bvproc
Replies: 1
Views: 4111

Sulcus Parametrization 2015 , bvproc

Hi, I am trying to run the 'Sulcus Parametrization 2015' function using BrainVISA 4.5 (OS X 10.11.4) from the command line. I saved a .bvproc process from the GUI and then I run it like: /Applications/brainvisa-4.5/bin/brainvisa -r file.bvproc but I got the following error messages: Loading toolbox ...
by f4bry
Thu Apr 07, 2016 7:42 am
Forum: BrainVISA
Topic: morphologist after freesurfer import
Replies: 13
Views: 13097

Re: morphologist after freesurfer import

For the DYLD_LIBRARY_PATH issue,:

I am running brainvisa from the terminal, setting the variables:

brainvisa/bin/python bv_env.py

and then running the GUI:

brainvisa/bin/./brainvisa

or the scripts:
brainvisa/bin/brainvisa -r *.bvproc

Thanks!
Fab
by f4bry
Thu Apr 07, 2016 7:38 am
Forum: BrainVISA
Topic: morphologist after freesurfer import
Replies: 13
Views: 13097

Re: morphologist after freesurfer import

Hi Denis, Yes, I am interested in sulci and I would like to import the FS ribbon. I think I didn't setup the scripts correctly and I was computing the segmentation using Morphologist. My initial steps were like: 1) Import from Freesurfer 2) Removing *.lock 3) Morphologist - Sulci recognition ...and ...
by f4bry
Mon Apr 04, 2016 11:41 pm
Forum: BrainVISA
Topic: morphologist after freesurfer import
Replies: 13
Views: 13097

Re: morphologist after freesurfer import

Hi,

I solved the .dylib issue by setting:
export DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:/Applications/brainvisa/lib

Thanks! :)
Fab
by f4bry
Mon Apr 04, 2016 7:20 pm
Forum: BrainVISA
Topic: morphologist after freesurfer import
Replies: 13
Views: 13097

Re: morphologist after freesurfer import

Hi Denis, Actually, using my local pc (Mac OS X 10.11.3) and BrainVISA 4.5 ( thank you for the new release! ) I get the following error when I try to import grey/white segmentation from FS: Process Import FreeSurfer grey/white segmentation to Morphologist started on 2016/04/04 11:15 Convert .mgz to...
by f4bry
Mon Apr 04, 2016 6:47 pm
Forum: BrainVISA
Topic: morphologist after freesurfer import
Replies: 13
Views: 13097

Re: morphologist after freesurfer import

Hi Denis,

The problem was that we were not really using the FS ribbon. But then, we figured out that after deleting the .lock files (an operation that we did), BrianVISA recomputes the segmentation.

Do we need the T1 if we convert the meshes from FS?

Thank you!
Fab
by f4bry
Wed Mar 23, 2016 3:45 am
Forum: BrainVISA
Topic: morphologist after freesurfer import
Replies: 13
Views: 13097

Re: morphologist after freesurfer import

Hi, Is it possible to import the segmentation maps and bias corrected images from Freesurfer instead of running the bias correction and Grey White classification process of Morphologist? (my main goal is the sulci labelling). Now, I am importing T1_orig, ribbon_img and Talairach tranformation. How e...
by f4bry
Fri Mar 11, 2016 10:35 pm
Forum: Anatomist
Topic: graph display properties
Replies: 6
Views: 16802

Re: graph display properties

Hi, I changed the default palette by adding the following command at the line ~330 palette=a.getPalette("Yellow-red-fusion") and then if isinstance( palette, a.APalette ): ag.setPalette( palette ,minVal=0.18, maxVal=0.72, absoluteMode=True) at line ~343 Thanks! Fab
by f4bry
Thu Mar 10, 2016 8:40 pm
Forum: Anatomist
Topic: graph display properties
Replies: 6
Views: 16802

Re: graph display properties

Hi, siCsvMapGraph.py is very useful! Would be possible to change the default palette in siCsvMapGraph.py , or to select a palette with a kind of 'siCsvMapGraph.py -palette-option', assigning also the min/max values? And, in my case there are always some 'unknown' objects that I have to delete manual...
by f4bry
Thu Feb 18, 2016 7:42 am
Forum: BrainVISA
Topic: Quality control of labelled sulci
Replies: 7
Views: 8429

Re: Quality control of labelled sulci

Hi, Without 3D hardware acceleration I got: vglrun /home/username/Applications/brainvisa/bin/bv_env ~/Applications/brainvisa/bin/python /home/username/Documents/testana.py Fontconfig error: "/etc/fonts/conf.d/10-scale-bitmap-fonts.conf", line 70: non-double matrix element Fontconfig error:...
by f4bry
Fri Feb 12, 2016 2:21 am
Forum: BrainVISA
Topic: Quality control of labelled sulci
Replies: 7
Views: 8429

Re: Quality control of labelled sulci

Hi Denis, I removed the libstdc++ from Brainvisa as described here http://brainvisa.info/forum/viewtopic.php?f=2&t=1745 Yes, I was running the script as you said: vglrun /home/username/Applications/brainvisa/bin/axon-runprocess ... Running your script 'testana.py' , with the libstdc++, and activ...