Search found 16 matches

by ericbarnhill
Thu Jun 21, 2012 2:48 pm
Forum: BrainVISA
Topic: Access to Freesurfer Subcortical meshes
Replies: 2
Views: 1757

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 ...
by ericbarnhill
Wed Apr 04, 2012 3:29 pm
Forum: Anatomist
Topic: Directional Cosines in Anatomist
Replies: 1
Views: 2824

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...
by ericbarnhill
Mon Mar 05, 2012 7:23 am
Forum: BrainVISA
Topic: brainvisa morphology extension
Replies: 7
Views: 5001

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.
by ericbarnhill
Wed Feb 29, 2012 12:16 pm
Forum: BrainVISA
Topic: fd4 and fd4_native morphometric models
Replies: 1
Views: 2347

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
by ericbarnhill
Mon Feb 13, 2012 3:30 pm
Forum: Anatomist
Topic: VTK plugin
Replies: 1
Views: 3208

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...
by ericbarnhill
Wed Feb 08, 2012 6:12 pm
Forum: Anatomist
Topic: PyAnatomist instantiation with bang line script
Replies: 1
Views: 3205

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 ...
by ericbarnhill
Tue Feb 07, 2012 4:08 pm
Forum: BrainVISA
Topic: Obtaining Sulcal Volume Information in 3.1?
Replies: 1
Views: 2031

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...
by ericbarnhill
Tue Feb 07, 2012 4:03 pm
Forum: BrainVISA
Topic: siGraph2Label 3.1 error
Replies: 2
Views: 1354

Re: siGraph2Label 3.1 error

You are correct, the -a was cut. Thank you for helping me with such an obvious problem.
by ericbarnhill
Fri Feb 03, 2012 4:09 pm
Forum: BrainVISA
Topic: siGraph2Label 3.1 error
Replies: 2
Views: 1354

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...
by ericbarnhill
Fri Jan 20, 2012 11:50 am
Forum: BrainVISA
Topic: SPAM seems to be missing file
Replies: 4
Views: 2104

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...
by ericbarnhill
Thu Jan 19, 2012 5:42 pm
Forum: BrainVISA
Topic: SPAM seems to be missing file
Replies: 4
Views: 2104

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...
by ericbarnhill
Wed Jan 18, 2012 3:57 pm
Forum: BrainVISA
Topic: SPAM seems to be missing file
Replies: 4
Views: 2104

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...
by ericbarnhill
Wed Jan 18, 2012 3:51 pm
Forum: BrainVISA
Topic: Cortical Folds Graph -- 3.1 as default
Replies: 2
Views: 1892

Re: Cortical Folds Graph -- 3.1 as default

This works, thank you!
by ericbarnhill
Tue Jan 17, 2012 1:07 pm
Forum: BrainVISA
Topic: Cortical Folds Graph -- 3.1 as default
Replies: 2
Views: 1892

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...
by ericbarnhill
Tue Jan 17, 2012 12:04 pm
Forum: BrainVISA
Topic: Error for non-admin users - siGraph2Label
Replies: 1
Views: 1308

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...

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