Hi,
The "head mesh" in morphologist 2012 looks to be out of order = the process goes well (as well as the previous and following steps).
Nevertheless, no "head...." file is created (corresponding to the head mesh which was quite beautiful for illustrative purposes)
Thanks
Josselin
Search found 62 matches
- Fri Oct 05, 2012 10:21 pm
- Forum: BrainVISA
- Topic: "Head Mesh" in Morphologist 2012
- Replies: 1
- Views: 4690
- Thu Feb 09, 2012 12:13 pm
- Forum: BrainVISA
- Topic: Morphologist 2012
- Replies: 1
- Views: 3819
Morphologist 2012
Hi, I have seen that in the new version of BV 4.2, the morphologist pipeline name has been changed to Morphologist "2012". From the changelog, it is not clear what are the changes to this pipeline. Which parts of this pipeline have been modified ? and do you recommend to re-run the pipelin...
- Sat Oct 08, 2011 9:07 pm
- Forum: BrainVISA
- Topic: Measuring bundle volume
- Replies: 4
- Views: 5844
Re: Measuring bundle volume
Thanks for your explanations,
Yes I already used this field (or the AImsRoiFeatures I can't remember).
I think this stat is useful to estimate the volume of a bundle. In the literature this kind of metric seems now more used than the the number of reconstructed fibers.
Josselin
Yes I already used this field (or the AImsRoiFeatures I can't remember).
I think this stat is useful to estimate the volume of a bundle. In the literature this kind of metric seems now more used than the the number of reconstructed fibers.
Josselin
- Mon Oct 03, 2011 5:14 pm
- Forum: BrainVISA
- Topic: Measuring bundle volume
- Replies: 4
- Views: 5844
Re: Measuring bundle volume
Hi, Thanks for your help. About this 'point_count' statistic: does it count the number of voxels crossed by fibers OR the number of total voxels included in the bundle i.e. if several fibers cross a single voxel, will this voxel be counted several times ? About your question about my usage of DTI pi...
- Sun Oct 02, 2011 5:52 pm
- Forum: BrainVISA
- Topic: Measuring bundle volume
- Replies: 4
- Views: 5844
Measuring bundle volume
Hi, I can't remember how I can get the "volume" of a bundle created with Brainvisa. By volume, I mean the number of voxels crossed by the bundles. Is it with comistBundleAnalysis where I can see this -o option: points_count: the total number of curves points in a bundle What do you mean by...
- Sun Jul 10, 2011 1:06 pm
- Forum: BrainVISA
- Topic: Hippocampus and amygdala segmentation (SACHA)
- Replies: 1
- Views: 4651
Hippocampus and amygdala segmentation (SACHA)
Hi, I have read papers about the Sacha module in Brainvisa (e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677639/ by Chupin et al., 2009). I would be interested in using it. Unfortunately, I can't find it anywhere in the Brainvisa website nor anywhere else. Do anyone know where I can find it ? T...
- Sun Nov 28, 2010 11:38 pm
- Forum: BrainVISA
- Topic: Bad segmentation of corpus callosum in T1 pipeline
- Replies: 1
- Views: 3251
Bad segmentation of corpus callosum in T1 pipeline
Dear all, I have a problem with the T1 pipeline with one subject. The T1 pipeline doesn't include in its mask a part of the corpus callosum (a dorsal and posterior part) I think it is mostly because of T1 bias correction as I can see the same bug on the hfiltered image I have tried to tweak the fiel...
- Tue Aug 31, 2010 10:13 pm
- Forum: BrainVISA
- Topic: .arg files improperly handled in BV4 for windows ?
- Replies: 6
- Views: 6958
Re: .arg files improperly handled in BV4 for windows ?
Hi Dominique, You were right, I tried to load the same bundle files (whole brain tractography) on different systems: -linux : no problem, whether the version of BV -windows : unable to correctly load the file, whether the version of BV What is more annoying is that processing through diffusion pipel...
- Wed Aug 11, 2010 6:06 am
- Forum: BrainVISA
- Topic: .arg files improperly handled in BV4 for windows ?
- Replies: 6
- Views: 6958
Re: .arg files improperly handled in BV4 for windows ?
Hi Isabelle, When I try to overlay my .bundles files on a .ima image in anatomist on Windows, I have the following warning message in the command line MS-DOS box: "OpenGL error tex:memoire insuffisante TexImage failed ~GLTexture - Bad GL texteure - 0" The bundles file is large (whole brain...
- Tue Aug 03, 2010 10:15 am
- Forum: BrainVISA
- Topic: .arg files improperly handled in BV4 for windows ?
- Replies: 6
- Views: 6958
Re: .arg files improperly handled in BV4 for windows ?
Hi, It is more sensible with .bundles file e.g. when I try to load a file called niania.bundles into Anatomist, it loads it, but I can't see any node in this object in anatomist. When I paste this bundles file onto its reference image, nothing appears in this image. furthermore, in brainvisa, when I...
- Fri Jul 23, 2010 5:51 pm
- Forum: BrainVISA
- Topic: skull stripping of T1, b0, T2 and DTI images
- Replies: 1
- Views: 3547
skull stripping of T1, b0, T2 and DTI images
Hello,
I would like to know if any process in Brainvisa is able to skull strip T1, b0, T2 and DTI images ? Else, which software do you recommend (BET/FSL, SPM8) ?
thanks !
Josselin
I would like to know if any process in Brainvisa is able to skull strip T1, b0, T2 and DTI images ? Else, which software do you recommend (BET/FSL, SPM8) ?
thanks !
Josselin
- Thu Jul 22, 2010 9:57 pm
- Forum: BrainVISA
- Topic: .arg files improperly handled in BV4 for windows ?
- Replies: 6
- Views: 6958
.arg files improperly handled in BV4 for windows ?
Hi, I have installed BV 4.0 on a windows xp laptop (with 4 GB RAM). It works fine except when I want to display .arg files: -in anatomist: I can't overlay correctly .arg files on templates -in brainvisa: processes using .arg files aren't working correctly (as in diffusion pipeline) I must note that ...
- Thu Jul 22, 2010 7:32 pm
- Forum: BrainVISA
- Topic: question about .brules files
- Replies: 2
- Views: 3762
question about .brules files
Hi, I have a question about .brules files. I use it in the "diffusion bundles transformation" component. The documentation in brainvisa is perfect except I can't find how you can "exclude" ROI i.e. = I have got a set of >100 ROI and I want to select bundles going through ROI n° 2...
- Thu Jun 17, 2010 5:14 am
- Forum: BrainVISA
- Topic: Error message in Tracking pipeline
- Replies: 7
- Views: 6268
Re: Error message in Tracking pipeline
Hello,
It occurs probably because in the menu "Brainvisa/preferences", you have not set your "userlevel" to "expert".
Josselin
It occurs probably because in the menu "Brainvisa/preferences", you have not set your "userlevel" to "expert".
Josselin
- Tue Jun 15, 2010 9:21 pm
- Forum: BrainVISA
- Topic: volume calculation
- Replies: 9
- Views: 7579
Re: volume calculation
Hi,
Thanks. Is the volume resuls given in mm3 or in voxels ?
Josselin
Thanks. Is the volume resuls given in mm3 or in voxels ?
Josselin