Search found 30 matches

by François Leroy
Thu Apr 21, 2016 4:23 pm
Forum: BrainVISA
Topic: no such table: _TRANSFORMATIONS_
Replies: 3
Views: 1751

Re: no such table: _TRANSFORMATIONS_

After updating all my databases, the error message disappeared. Thanks!
by François Leroy
Tue Apr 19, 2016 12:39 pm
Forum: BrainVISA
Topic: no such table: _TRANSFORMATIONS_
Replies: 3
Views: 1751

no such table: _TRANSFORMATIONS_

Hi, I am looking at some files processed through the baby pipeline and I am getting this error message on and on: "no such table: _TRANSFORMATIONS_ Cannot load referential and transformations information with object xxx" I tried to do a "check database" and "update database&...
by François Leroy
Thu Oct 09, 2014 9:59 am
Forum: BrainVISA
Topic: Conflict with identical uuid across multiple files
Replies: 2
Views: 2521

Re: Conflict with identical uuid across multiple files

Thanks Denis for this information. Here is an example of saving a file without uuid duplication. Suppose you have created some array (eg arr_seg) and that you want to save it with a given file name (eg seg_filename) by using a reliable image header which includes its own uuid (eg vol_mri): vol_seg =...
by François Leroy
Mon Oct 06, 2014 9:40 am
Forum: BrainVISA
Topic: Conflict with identical uuid across multiple files
Replies: 2
Views: 2521

Conflict with identical uuid across multiple files

Hi brain-wisers, When running the baby pipeline toolbox, I got an error message several times related to conflict between file uuids. The error message says there is a file with the same uuid than the file being processed by the pipeline. I checked the uuid in the .minf of these files and found that...
by François Leroy
Tue Mar 18, 2014 11:21 am
Forum: BrainVISA
Topic: Pipeline Release and Morphometry Measurements
Replies: 2
Views: 2467

Re: Pipeline Release and Morphometry Measurements

Hi Denis, I just spoke with Clara. There are indeed minor changes to the brain morphometry. 1) you're right: the slight brain reduction and dilation according to Z / X, respectively, probably come from different normalization procedures, ie non-linear (using SPM, 2012 pipeline) or linear (using stan...
by François Leroy
Tue Mar 11, 2014 3:20 pm
Forum: BrainVISA
Topic: Pipeline Release and Morphometry Measurements
Replies: 2
Views: 2467

Pipeline Release and Morphometry Measurements

Hi, In my datasets, the morphologist pipelines 2007 and 2012 have been applied to dbA and dbB, respectively. When computing sulcal depth (with my own piece of software), I have larger sulcal depth in dbB (2012) than in dbA (2007). This could be due to many issues, including a change of software or h...
by François Leroy
Mon Dec 09, 2013 6:04 pm
Forum: BrainVISA
Topic: Importing Free Surfer thickness surface file
Replies: 1
Views: 2403

Importing Free Surfer thickness surface file

Hi, This is more a comment than a question. We used Free Surfer to compute cortical thickness across the brain. After running Free Surfer, data were imported in Brainvisa (in order to compute sulci) using the "Import from Free Surfer to T1 Pipeline" tool. Then we tried to import the thickn...
by François Leroy
Wed Jun 26, 2013 1:22 pm
Forum: AIMS
Topic: Nifti Header with Talairach or MNI coordinates
Replies: 2
Views: 5605

Re: Nifti Header with Talairach or MNI coordinates

Great! It worked all fine! Thanks a lot Denis.
by François Leroy
Tue Jun 25, 2013 2:28 pm
Forum: AIMS
Topic: Nifti Header with Talairach or MNI coordinates
Replies: 2
Views: 5605

Nifti Header with Talairach or MNI coordinates

Hi, Let's say I would like to send a nifti volume file to a remote collegue. He strongly asked me to save the Talairach or MNI coordinates within the nifti header. How should I proceed? Usually, when looking at a T1 MRI (eg T1volume.nii) that has been imported in Brainvisa, getting Talairach or MNI ...
by François Leroy
Wed Nov 07, 2012 4:26 pm
Forum: Anatomist
Topic: Anatomist crash when viewing a nifti or a mesh image
Replies: 1
Views: 3993

Anatomist crash when viewing a nifti or a mesh image

Hi, When running Anatomist 4.4.0 on linux Ubuntu, it crashes as soon as I want to load a nifti image or a mesh within an Anatomist window (in order to see it). I guess my Nvidia card has not the proper set up. What should I change within this set up? Here is the full error log: QGLContext::makeCurre...
by François Leroy
Wed Sep 12, 2012 12:24 pm
Forum: BrainVISA
Topic: gyral parcellation : no gyral texture
Replies: 2
Views: 1511

Re: gyral parcellation : no gyral texture

Great! We looked at timestep 2 and we got the gyral parcellation. That's fine.
by François Leroy
Wed Sep 12, 2012 12:22 pm
Forum: BrainVISA
Topic: cortical surface parameterization : no gyral parcels
Replies: 4
Views: 2488

Re: cortical surface parameterization : no gyral parcels

Thank you for your help. Because I cannot get the old pipeline to work, and that the 2012 pipeline is not ready yet, I think we will choose Arnaud Cachia's gyral parcellation (the other parcellation tool within Brainvisa). Our idea is to use this other gyral parcellation as a starting point. Then, w...
by François Leroy
Fri Sep 07, 2012 1:24 pm
Forum: BrainVISA
Topic: gyral parcellation : no gyral texture
Replies: 2
Views: 1511

gyral parcellation : no gyral texture

Hi, We've been trying the Arnaud Cachia's "Gyral parcellation" process on one left hemisphere. We succeeded in displaying the gyral output graph "<subject>_L_gyri_default_session_manual.arg". We can see all the gyral regions in colors. That's great! But we are more interested in ...
by François Leroy
Fri Sep 07, 2012 1:13 pm
Forum: BrainVISA
Topic: cortical surface parameterization : no gyral parcels
Replies: 4
Views: 2488

cortical surface parameterization : no gyral parcels

Hi, We've been trying the Cortical Surface Parameterization pipeline on one left hemisphere with no success. Both texture files "<subject>_L_gyri.tex" and "<subject>_L_gyri_regul.tex" displayed only one or two sulci (in the insula). As inputs, we used the "default_session_ma...
by François Leroy
Mon Jun 18, 2012 1:45 pm
Forum: Anatomist
Topic: access to local texture intensity
Replies: 1
Views: 4548

access to local texture intensity

Hi,
Once I created a "Textured surface", ie, by combining a mesh file and a gifti texture file (FusionTexSurfMethod), is it possible to get the texture intensity when I click at a given location of the object in a 3D window?
Thanks for your help,
Francois

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