BrainVISA

Hi Denis, Hi Joost, I guess VipSkeleton doesn't work because you have provided the same input, a binary image, as -i and -g options. -g is expected to be a grey level image, used for saddle points extraction: here it is a binary image, so the saddle points are crap. Did you get this command from the...

Hi Isa, can i send the complete input and output (zipped nifti format) file from my VipSkeleton command line to your (private) email address? that will give you the chance to replicate this error output. you can send me an email (joost.janssen76@gmail.com) and i will reply with the input and output ...

Hi, - version 4.2.1 - stamp: Linux neurojoost 2.6.32-41-generic #94-Ubuntu SMP Fri Jul 6 18:00:34 UTC 2012 x86_64 GNU/Linux - command: VipSkeleton -sk s -im a -gcs 2 -e 0.5 -i tmp_white.nii -so tmp_skel_1mm -g tmp_white - terminal output: Reading tmp_white.nii... =============== SKELETONIZATION ====...

Hi,

1. FreeSurfer does not -by default- produce any subcortical meshes. one'll have to generate these from the aseg-segmentations using external tools.

2. i have post on going from FS -> BV. it may have some useful details.

merci,
-joost

Hi, i created ventricle segmentation volumes in NIFTI format outside BrainVisa (using SPM8). when i open the ventricle segmentation volume in Anatomist, it's referential (Talairach AC/PC Anatomist) is different from the nobias_T1 image (Raw T1 MRI) and i cannot overlay the two images (see attached o...

Hi, >In fact, the Freesurfer coordinate system seems very good, but as far as I know in Freesurfer when you read coordinates on the sphere, you read according to the >freesurfer spherical atlas. >When you compute data in freesurfer from subjectA_?hsphere to subjectA_?hsphere.reg, actually the mesh s...

Hi, sorry, it's line 21 not 15 in talairach.lta FreeSurfer produces surfaces (e.g. ?h.pial/white) in the subject's native image space, no "unwarping" is applied. Freesurfer resamples original T1 data to 1x1x1mm resolution before processing it (conform). The problem was just between the coo...

Hi, the answer is: in the freesurfer subject dir/mri/transforms there's a talairach.lta file; the 15th line has 3 coordinates in the RAS coordinate system. if you want to move a freesurfer surface to brainvisa you have to add these coordinates to the original freesurfer surface coordinates. thereaft...

Hi, we solved our problem with some Matlab-magic, i.e. the *LWhite.mesh and lh.r.aims.white.mesh of the same subject are in the same coordinate space. it may be hard to appreciate from the attached .png but i assure you that it's true :-). let me know if anyone's interested in doing this. merci, -jo...

Hi, attached is a .png of Anatomist: - 2 white matter meshes of the same subject: 1. *Lwhite.mesh generated in Morphologist Pipeline; 2. lh.r.aims.white.mesh (from the FreeSurfer pipeline, resampled and in Aims Referential. as you can see the meshes do not overlap, i would like to move the lh.r.aims...

Hi, attached is a .png of Anatomist: - 2 white matter meshes of the same subject: 1. *Lwhite.mesh generated in Morphologist Pipeline; 2. lh.r.aims.white.mesh (from the FreeSurfer pipeline, resampled and in Aims Referential. as you can see the meshes do not overlap, i would like to move the lh.r.aims...

Hi,

can i change the colour of the background in a Anatomist 3D terminal? it's default is white but i'd like a different colour.

merci,
-joost

Hi, stamp: BV version 4.2.1, Ubuntu 64-bits. i'm trying to use the Gyral Parcellation process (Cortical Surface->old) using SOMA (Run in parallel). this is the output given for 1 subject under the 'standard output' tab: Loading toolbox RII Loading toolbox brainrat Loading toolbox connectomist Loadin...

Hi, thanks. >I can confirm that you can't do a fusion between meshes coming from Morphologist and texture data coming from FreeSurfer. >The way to compute them are different, so that those data don't share the same structure. You can't do a fusion between the lh.aparc.annot.tex / lh.r.aparc.annot.te...

Hi, >For the time being, this is not possible because when you match a texture and a mesh, many precautions are necessary : >- to make sure that texture and mesh are in the same referentiel >- that the texture can be matched on the mesh, if mesh and texture have the same point number (so one texture...