Search found 86 matches

by joost
Tue Apr 17, 2018 12:34 pm
Forum: BrainVISA
Topic: QC on large database
Replies: 1
Views: 11461

QC on large database

Hi,

To those that have experience with very large 9'n') BrainVisa databases: I used Morphologist QC table but is there anything else? Obviously I can do number-based outlier detection (akin to ENIGMA) but is there anything else within BrainVisa that I missed?

Merci!
-joost
by joost
Fri Mar 03, 2017 10:51 am
Forum: BrainVISA
Topic: install on Ubuntu 16.04.2 LTS
Replies: 4
Views: 8844

Re: install on Ubuntu 16.04.2 LTS

if i type Qt at the command line I get:
Fatal Python error: Py_Initialize: Unable to get the locale encoding
ImportError: No module named 'encodings'
by joost
Thu Mar 02, 2017 5:28 pm
Forum: BrainVISA
Topic: install on Ubuntu 16.04.2 LTS
Replies: 4
Views: 8844

Re: install on Ubuntu 16.04.2 LTS

Some further specs of my machine.
merci
by joost
Thu Mar 02, 2017 3:45 pm
Forum: BrainVISA
Topic: install on Ubuntu 16.04.2 LTS
Replies: 4
Views: 8844

Re: install on Ubuntu 16.04.2 LTS

just adding: i am using Linux 64 bits (glibc 2.6) (built on Mandriva 2008)
merci
by joost
Thu Mar 02, 2017 3:40 pm
Forum: BrainVISA
Topic: install on Ubuntu 16.04.2 LTS
Replies: 4
Views: 8844

install on Ubuntu 16.04.2 LTS

Hi, I'm trying to get brainvisa working on Ubuntu Xenial. in my .bashrc i have: function brainvisa_setup { . /opt/brainvisa/bin/bv_env.sh /opt/brainvisa } when i start brainvisa the update database window frame opens, but then hangs. i see no python rubbing in my 'top'. this is the on screen output:...
by joost
Mon Oct 31, 2016 12:43 pm
Forum: BrainVISA
Topic: AimsSulcalLines
Replies: 4
Views: 8135

Re: AimsSulcalLines

Happy to send a Brainvisa subject dir for testing. Just let me kow.

Merci
by joost
Mon Oct 31, 2016 12:15 pm
Forum: BrainVISA
Topic: AimsSulcalLines
Replies: 4
Views: 8135

Re: AimsSulcalLines

Hi,

All. Also, FWIW, it happens under different Ubuntu distros (13.10, 14.10, 16.4).

Merci
by joost
Mon Oct 31, 2016 10:21 am
Forum: BrainVISA
Topic: AimsSulcalLines
Replies: 4
Views: 8135

AimsSulcalLines

Dear Denis, Brainvisa4.5 Ubuntu 14.10 In BrainVisa4.5 I'm running AimsSulcalLines with "-m 4" and it produces a segmentation fault after running for quite some time. AimsSulcalLines with "-m 3" (NeuroImage method) runs fine. Could you try to replicate this and let me know? Merci
by joost
Mon Oct 03, 2016 10:48 am
Forum: BrainVISA
Topic: Converting Freesurfer labels to AIMS textures error
Replies: 2
Views: 4602

Re: Converting Freesurfer labels to AIMS textures error

sorry, little typo Hi, I'm using the 'Converting Freesurfer labels to AIMS textures' UI (from the Freesurfer toolbox). I first select the lh.white.gii from my Freesurfer-database without any problem. The other mandatory inputs are also automatically found EXCEPT the 'database' variable (it remains e...
by joost
Mon Oct 03, 2016 10:47 am
Forum: BrainVISA
Topic: Converting Freesurfer labels to AIMS textures error
Replies: 2
Views: 4602

Converting Freesurfer labels to AIMS textures error

Hi, I'm using the 'Converting Freesurfer labels to AIMS textures' UI (from the Freesurfer toolbox). I first select the lh.white.gii from my Freesurfer-database with any problem. The other mandatory inputs are automatically found EXCEPT the 'database' variable (it remains empty). Selecting it manuall...
by joost
Thu Oct 08, 2015 3:39 pm
Forum: BrainVISA
Topic: cortical thickness along a sulcus
Replies: 1
Views: 4930

cortical thickness along a sulcus

Cortical thickness measurements in BrainVisa is restricted to a sulcus, does this mean that sulcal _basins_ are labelled in concordance with the sulcal labelling of BrainVisa and then the average Laplacian-based thickness is computed over all points of each labelled basin? Or is the measurement rest...
by joost
Wed Jan 23, 2013 3:59 pm
Forum: BrainVISA
Topic: 3.0: Tmtktri_Mesh.mesh versus 3.1: aims_Tmtktri.mesh
Replies: 0
Views: 30721

3.0: Tmtktri_Mesh.mesh versus 3.1: aims_Tmtktri.mesh

Hi, BV v.4.2.1 in Morphologist one can choose to generate 3.0 and 3.1 graph files. these co-produce a Tmtktri_Mesh.mesh (v3.0) or an aims_Tmtktri.mesh (v3.1). i think there is (are?) some difference(s) in the file structure between these two files (perhaps the numbering of meshes in both files, e.g....
by joost
Wed Jan 23, 2013 11:55 am
Forum: BrainVISA
Topic: Issue with the mesh format for the latest version
Replies: 5
Views: 7350

Re: Issue with the mesh format for the latest version

Hi Denis,

could you give a concrete example of how to use python to update the normals for an existing brainvisa mesh?

merci,
-joost
by joost
Mon Nov 12, 2012 4:24 pm
Forum: BrainVISA
Topic: Hulljunctionlength
Replies: 1
Views: 3689

Hulljunctionlength

Hi,

brainvisa 4.2.1

for +100 subjects i looked at 'Hulljunctionslength' *summed over all sulci of both hemispheres* and found values ranging between 6589-8701, are these values normal and if so, what unit are they?

merci,
-joost
by joost
Mon Oct 29, 2012 4:03 pm
Forum: BrainVISA
Topic: Database problem
Replies: 1
Views: 4191

Database problem

Hi, version: BrainVisa 4.30 platform: Ubuntu i'm working under Ubuntu, i'm trying to add a (FreeSurfer-)database (Brainvisa->Preferences->Databases->Add) which is stored *on a Windows system*. i have full write and read access to this Windows-dir (e.g. from Ubuntu i can create dirs and delete dirs i...