Hi,
I did some tests with my data and I can give you additional information.
In fact you don't need to resample data because all information are written in the headers.
In order to resolve the problem, you can process by two different ways:
-> The FIRST is very simple, you can use the 001.nii file instead of T1.nii or orig.nii to run Morphologist. This allows:
1) to avoid to work with resampled data (volume size: 256x256x256; voxel size : 1x1x1)
2) data will be in the initial space (referential of ../mri/orig/001.nii), so you could superimpose both meshes.
-> The SECOND, if you work with ../mri/T1.nii or ../mri/orig.nii, in order to superimpose meshes, you could handle the referential manager of Anatomist instead of resampling data. Anatomist propose a powerful tool to manage and to handle referantials without to resample data. Very often, you can find information in the part of header. Anatomist can read this information (for example transformation for the "scanner-based anatomical coordinates").
- "read information": drag and drop your volume into a browser window
- "load information from file header": right-click on the volume, then select the "referential -> load information from file header. Note that data are just modify for the display, not on the hard disk.
I assume that the following lines could resolve your problem without resample your data:
STEP 1: Load in Anatomist (open an anatomist session without BrainVISA)
- M1: load mesh computed by morphologist for instance T1_Lwhite.mesh
- M2: load mesh converted by the freesurfer pipeline in BrainVISA, lh.r.aims.white.mesh
- Anat 1: load T1.nii + "load information from file header" (see above)
- Anat 2: load 001.nii + "load information from file header"
STEP 2:
- Put M1 in the referential of Anat1 by right-clicking -> referential -> load the correct color
- Put M2 in the referential of Anat2 by right-clicking -> referential -> load the correct color
STEP 3: Load an identity transformation between both referentials:
- Open Settings -> Referential window
- Simultaneously, click on 'crtl' key + draw a line between both referantials called "scanner-based" (before pass the mouse on points of color to know their names)
SETP 4: Visualize
- Put M1 and M2 in the same 3D window
-
Change the referential of window by clicking on the line of the top in the 3D window. By default, this line is red, now use a color corresponding to one of "scanner based"
For the further version of toolbox, these steps could be automatically managed by BrainVISA.
Notes:
1) When you use Anatomist without BrainVISA, you manage yourself the referantials. But when you use BrainVISA and that you open Anatomist with BrainVISA, then some referentials are managed by BrainVISA. Automatic and magic things will happen
2) If a mesh becomes black: "mesh -> click-right -> geometry -> invert polygon orientation"
3) More information about referentials:
http://brainvisa.info/doc/aimsdata-4.2/ ... /ch06.html
http://brainvisa.info/doc/anatomist-4.2 ... /ch04.html
http://brainvisa.info/doc/anatomist-4.2 ... /ch08.html
Isa