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
Search found 29 matches
- Thu Nov 15, 2018 8:27 pm
- Forum: BrainVISA
- Topic: 'SelectByNomenclature' script
- Replies: 3
- Views: 15681
- Wed Nov 07, 2018 8:30 pm
- Forum: BrainVISA
- Topic: 'SelectByNomenclature' script
- Replies: 3
- Views: 15681
'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...
- Fri Dec 16, 2016 7:37 pm
- Forum: BrainVISA
- Topic: Sulci Curvature Stats
- Replies: 2
- Views: 7769
Re: Sulci Curvature Stats
Hi Denis,
Very clear, thank you so much!
Fab
Very clear, thank you so much!
Fab
- Fri Dec 16, 2016 5:27 am
- Forum: BrainVISA
- Topic: Sulci Curvature Stats
- Replies: 2
- Views: 7769
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
How 'Sulci Curvature Stats' tool computes the curvature? Is it the mean curvature over all the sulcal mesh vertices?
Thank you,
Fab
- Wed Aug 10, 2016 2:30 am
- Forum: BrainVISA
- Topic: Sulcus Parametrization 2015 , bvproc
- Replies: 1
- Views: 4185
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 ...
- Thu Apr 07, 2016 7:42 am
- Forum: BrainVISA
- Topic: morphologist after freesurfer import
- Replies: 13
- Views: 13351
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
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
- Thu Apr 07, 2016 7:38 am
- Forum: BrainVISA
- Topic: morphologist after freesurfer import
- Replies: 13
- Views: 13351
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 ...
- Mon Apr 04, 2016 11:41 pm
- Forum: BrainVISA
- Topic: morphologist after freesurfer import
- Replies: 13
- Views: 13351
Re: morphologist after freesurfer import
Hi,
I solved the .dylib issue by setting:
export DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:/Applications/brainvisa/lib
Thanks!
Fab
I solved the .dylib issue by setting:
export DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:/Applications/brainvisa/lib
Thanks!
Fab
- Mon Apr 04, 2016 7:20 pm
- Forum: BrainVISA
- Topic: morphologist after freesurfer import
- Replies: 13
- Views: 13351
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...
- Mon Apr 04, 2016 6:47 pm
- Forum: BrainVISA
- Topic: morphologist after freesurfer import
- Replies: 13
- Views: 13351
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
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
- Wed Mar 23, 2016 3:45 am
- Forum: BrainVISA
- Topic: morphologist after freesurfer import
- Replies: 13
- Views: 13351
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...
- Fri Mar 11, 2016 10:35 pm
- Forum: Anatomist
- Topic: graph display properties
- Replies: 6
- Views: 18673
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
- Thu Mar 10, 2016 8:40 pm
- Forum: Anatomist
- Topic: graph display properties
- Replies: 6
- Views: 18673
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...
- Thu Feb 18, 2016 7:42 am
- Forum: BrainVISA
- Topic: Quality control of labelled sulci
- Replies: 7
- Views: 8567
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:...
- Fri Feb 12, 2016 2:21 am
- Forum: BrainVISA
- Topic: Quality control of labelled sulci
- Replies: 7
- Views: 8567
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...