Search found 16 matches
- Thu Jun 21, 2012 2:48 pm
- Forum: BrainVISA
- Topic: Access to Freesurfer Subcortical meshes
- Replies: 2
- Views: 4653
Access to Freesurfer Subcortical meshes
Greetings, I have been using the "Freesurfer to T1 pipeline" here with success, adding the sulcal analyses to brains already processed here in Freesurfer for other projects. I cannot actually go right to the T1 pipeline as the software indicates, I get a data lock error. But it is okay, I ...
- Wed Apr 04, 2012 3:29 pm
- Forum: Anatomist
- Topic: Directional Cosines in Anatomist
- Replies: 1
- Views: 11037
Directional Cosines in Anatomist
Hello, I am wondering if Anatomist uses the directional cosine information when it loads brains. In one project have lots of sagittal scans with orientation 0\1\0\0\0\-1 and they come into anatomist with a saggital view when I choose axial window. Of course when I set the AC/PC for the pipeline it b...
- Mon Mar 05, 2012 7:23 am
- Forum: BrainVISA
- Topic: brainvisa morphology extension
- Replies: 7
- Views: 10624
Re: brainvisa morphology extension
I installed these extensions in 4.2, they seem fine to me. There are some files that unpack to the axon-4.1 share folder, I moved them to the axon-4.2 and everything seemed to run fine.
- Wed Feb 29, 2012 12:16 pm
- Forum: BrainVISA
- Topic: fd4 and fd4_native morphometric models
- Replies: 1
- Views: 4881
fd4 and fd4_native morphometric models
Hello,
I see that in the statistics there is a default model called fd4 and a second option called fd4_native . Does this mean that the default statistics are in Talairach space but they can also be produced for native space? Or does it mean something else?
Thanks,
Eric
I see that in the statistics there is a default model called fd4 and a second option called fd4_native . Does this mean that the default statistics are in Talairach space but they can also be produced for native space? Or does it mean something else?
Thanks,
Eric
- Mon Feb 13, 2012 3:30 pm
- Forum: Anatomist
- Topic: VTK plugin
- Replies: 1
- Views: 5324
VTK plugin
Greetings, I see that in 2009 a VTK plug-in was added to Anatomist. Is it possible to import and export anatomist meshes from/to .vtk? It does not appear possible within the ordinary save window. If I append the ".vtk" extension in the save window my file is a GIFTi ending in ".vtk.gi...
- Wed Feb 08, 2012 6:12 pm
- Forum: Anatomist
- Topic: PyAnatomist instantiation with bang line script
- Replies: 1
- Views: 5315
PyAnatomist instantiation with bang line script
Greetings, I want to create a PyAnatomist script that will save a series of .mesh as a .ply . (Actually I would prefer a .vtk but that is a second question.) All the steps work fine in the IPython interactive environment. However when I put them in a small script with bang line the instantiation of ...
- Tue Feb 07, 2012 4:08 pm
- Forum: BrainVISA
- Topic: Obtaining Sulcal Volume Information in 3.1?
- Replies: 1
- Views: 4518
Obtaining Sulcal Volume Information in 3.1?
Greetings and congratulations on the new release. I see that the morphometry statistics models for the 3.1 graphs no longer have a volume statistic. Our plan for the studies was to look at volume as well as surface area, length, and the depth stats. If I want to look at sulcus volumes, would you rec...
- Tue Feb 07, 2012 4:03 pm
- Forum: BrainVISA
- Topic: siGraph2Label 3.1 error
- Replies: 2
- Views: 4216
Re: siGraph2Label 3.1 error
You are correct, the -a was cut. Thank you for helping me with such an obvious problem.
- Fri Feb 03, 2012 4:09 pm
- Forum: BrainVISA
- Topic: siGraph2Label 3.1 error
- Replies: 2
- Views: 4216
siGraph2Label 3.1 error
Hello, This is a new error I am getting with siGraph2Label now that we are successfully using Cortical Folds Graph 3.1 . I am wondering if you can help me figure out what is wrong. Code: ./siGraph2Label -g $LFOLDSPATH -tr $TRLPATH label -o $CSPATH/CS-L.ima -b aims_ss -b aims_bottom -b aims_other Out...
- Fri Jan 20, 2012 11:50 am
- Forum: BrainVISA
- Topic: SPAM seems to be missing file
- Replies: 4
- Views: 6111
Re: SPAM seems to be missing file
You are correct, I used "clean old database" a few days ago. There were some duplicate files around in my database that were causing me trouble and I thought it might help. It definitely trashed a lot of files. I just now replaced the shared folder with one from a clean installation, and t...
- Thu Jan 19, 2012 5:42 pm
- Forum: BrainVISA
- Topic: SPAM seems to be missing file
- Replies: 4
- Views: 6111
Re: SPAM seems to be missing file
Hello again, I would like to add more information: Cortical Fold Arg 3.0 also faulted because it was looking for a folder called /share/brainvisa-share-4.1/nomenclature/syntax/ This folder was not there. However, I found it in /share/brainvisa-share-4.1/trash/nomenclature/syntax I moved it out of th...
- Wed Jan 18, 2012 3:57 pm
- Forum: BrainVISA
- Topic: SPAM seems to be missing file
- Replies: 4
- Views: 6111
SPAM seems to be missing file
Hello, I am trying to get all my users set to use SPAM as default for the sulci. The "Sulci Recognition" module is giving me an error message regarding a missing file. It is true, I am missing the file -- but I just re-installed the software with the module "SPAM Models Installation&q...
- Wed Jan 18, 2012 3:51 pm
- Forum: BrainVISA
- Topic: Cortical Folds Graph -- 3.1 as default
- Replies: 2
- Views: 4989
Re: Cortical Folds Graph -- 3.1 as default
This works, thank you!
- Tue Jan 17, 2012 1:07 pm
- Forum: BrainVISA
- Topic: Cortical Folds Graph -- 3.1 as default
- Replies: 2
- Views: 4989
Cortical Folds Graph -- 3.1 as default
Salut encore, If you don't mind one more question for now... Unless you think I should keep using Cortical Fold Graph 3.0, I would like Morphologist to default to 3.1 so the BSc students have it automatically. It is no problem to go into CorticalFoldsGraphGeneral.py and change the selection bit like...
- Tue Jan 17, 2012 12:04 pm
- Forum: BrainVISA
- Topic: Error for non-admin users - siGraph2Label
- Replies: 1
- Views: 3894
Error for non-admin users - siGraph2Label
Salut et bonne année, We are getting ready to start our sulci studies here. I am trying to set up several non-administrative users with access to BrainVISA, a common database, and related scripts and modules. I started getting an error with siGraph2Label. So this may be a problem with permissions or...