Search found 13 matches

by atsui
Thu Aug 22, 2013 7:02 am
Forum: BrainVISA
Topic: missing anatomist module after source build
Replies: 2
Views: 2338

Re: missing anatomist module after source build

Hi Denis, It looks like your hypothesis is right. I am able to run anatomist, but there is no python menu. I've attached a screenshot of the modules list from my copy of anatomist. I've compared it to the anatomist from a binary distribution I've downloaded it looks like there are many modules missi...
by atsui
Thu Aug 22, 2013 12:45 am
Forum: BrainVISA
Topic: missing anatomist module after source build
Replies: 2
Views: 2338

missing anatomist module after source build

Hi, I built the latest release of BrainVISA (4.3) from source using bv_maker. Next, I go to my build dir and run bv_env to generate environment variables that I source into my bash shell, and then I run brainvisa. The program seems to work, except certain tools are greyed out. Specifically, in Morph...
by atsui
Mon Oct 22, 2012 12:08 am
Forum: BrainVISA
Topic: Cingular pole template available?
Replies: 1
Views: 1921

Cingular pole template available?

Hello,

I am curious if the cingular pole template is made available with the Brainvisa distribution or elsewhere? Also, I was unsure how the insular pole was segmented. Is there a particular process in Brainvisa that I should take a look at?

Thanks,

--Alex
by atsui
Mon Oct 08, 2012 5:04 am
Forum: BrainVISA
Topic: Harmonic parameterization of the cortical surface
Replies: 1
Views: 1531

Harmonic parameterization of the cortical surface

Hi, I'm interested in applying the method in the 2011 paper on Model-Driven Harmonic Parameterization of the Cortical Surface to some of our meshes. Before asking further, I noticed that a previous thread mentioned there is the 2012 cortical surface parameterization pipeline is in progress. Is that ...
by atsui
Thu Jun 07, 2012 7:52 am
Forum: BrainVISA
Topic: Issue with the mesh format for the latest version
Replies: 5
Views: 2955

Re: Issue with the mesh format for the latest version

Hello, I just wanted to add some context to the issue that Peter is referring to. I am using his RIC toolbox to estimate cortical thickness, which makes use of gray matter and white matter meshes generated at the end of the Morphologist 2012 pipeline. It seems like it asserts something about the mes...
by atsui
Tue Jun 05, 2012 5:28 pm
Forum: AIMS
Topic: AimsInflate doesn't save sequence [solved]
Replies: 5
Views: 6083

Re: AimsInflate doesn't save sequence [solved]

Thanks Olivier, This is helpful. I think I will follow your idea for the time being, but I'd like to teach myself a bit of python programming as well. I think I will look into doing some python programming using PyAIMS. There's an example here http://brainvisa.info/doc/pyaims-4.2/examples/mesh_test....
by atsui
Tue Jun 05, 2012 9:27 am
Forum: AIMS
Topic: AimsInflate doesn't save sequence [solved]
Replies: 5
Views: 6083

Re: AimsInflate doesn't save sequence

Wow, that was easy. Thanks for pointing that out for me!

To follow up, how can I extract an individual mesh at a particular time point from the .mesh file containing the sequence, either from Anatomist or AIMS?

--Alex
by atsui
Tue Jun 05, 2012 4:32 am
Forum: AIMS
Topic: AimsInflate doesn't save sequence [solved]
Replies: 5
Views: 6083

AimsInflate doesn't save sequence [solved]

Hi, I'm trying to save a sampling of the inflation sequence generated by AimsInflate, but the intermediate meshes in the sequence don't appear. Here is the command that I issue: $ AimsInflate -i 10100_Lhemi.mesh -o inflate_500.mesh -t 500 -Kn 0.01 -Ksp 0.01 -Ksm 0.5 -c curvature_500.tex -S Parameter...
by atsui
Mon May 07, 2012 5:49 am
Forum: BrainVISA
Topic: GeneralImport image flipped
Replies: 1
Views: 1391

GeneralImport image flipped

Hi again, I'm using Data Management > T1 MRI > GeneralImport to import my own Left Grey White Mask for use in mesh generation in the Morphologist 2012 pipeline, but it seems like the mask is flipped with respect to left and right. Maybe it has something to do with the input_spm_orientation setting b...
by atsui
Sun May 06, 2012 7:23 am
Forum: BrainVISA
Topic: Anatomist Show Volume problem
Replies: 2
Views: 1553

Re: Anatomist Show Volume problem

Not sure if this is useful information but I just wanted to report that somehow, after many combinations of clicking the eye icon and closing Anatomist, the image finally loads when I click the eye icon, and if I click the eye icon again, the image and object will unload itself. Basically, if I don'...
by atsui
Sun May 06, 2012 6:03 am
Forum: BrainVISA
Topic: Anatomist Show Volume problem
Replies: 2
Views: 1553

Anatomist Show Volume problem

Hi, I'm having a problem where Anatomist Show Volume does not display my image. When I have a raw T1 MRI specified, I click the eye icon on the right, and I expect Anatomist to show me my T1. What actually happens is that Anatomist pops up, an object gets loaded into the list (middle window in the s...
by atsui
Mon Apr 16, 2012 8:57 pm
Forum: BrainVISA
Topic: Topology of cortical mesh
Replies: 4
Views: 2044

Re: Topology of cortical mesh

Denis,

Yes, I am using the G/W meshes. I re-ran the mesh generation using the 2012 procedures in BrainVISA 4.2.1. The meshes look a lot nicer and the handles that made some meshes non-genus zero went away.

Thanks for the tip,

--Alex
by atsui
Fri Apr 13, 2012 6:37 pm
Forum: BrainVISA
Topic: Topology of cortical mesh
Replies: 4
Views: 2044

Topology of cortical mesh

Hello, I'm interested in cortical surface parameterization and was using Brainvisa to generate brain meshes for this purpose. The problem is that the resulting meshes are not necessarily genus zero surfaces -- upon closer inspection, there are handles hidden in an otherwise well-behaved looking mesh...

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