Create Surface-Based Functional Data (Projection of fMRI Data onto the Cortical Surface)
Create Surface-Based Functional Data (Projection of fMRI Data onto the Cortical Surface)Projection of fMRI data onto cortical surfaces using convolution kernels
This process aims at creating surface-based maps out of volume-based fMRI data. It takes as input a 4D volume, containing an fMRI (BOLD) timeserie (fmri_data parameter), and a mesh of the grey / white matter interface (white_mesh parameter), like the one produced by Morphologist pipeline. It generates a map (also referred as texture, timeserie_texture parameter) assigning each node of the mesh with a functional timecourse. This map can then be taken as an input of the Surface-based Structural Group Analysis pipeline.
This pipeline consists as follows :
- first it computes an average 3D volume from the functional 4D volume (step 1)
- this average volume is used as a reference template to register the white_mesh surface with (step 2 - 3).
- from the white_mesh surface, a set of convolution kernels is computed (step 4). Check that the kernels are produced at the same resolution as the input fMRI volumes !
- the final process takes the kernels, the fMRI 4D volume and the cortical mesh to produce a surface-based fMRI map
The whole method is described in :
G. Operto, R. Bulot, J.-L. Anton, O. Coulon, Projection of fMRI data onto the cortical surface using anatomically-informed convolution kernels, NeuroImage, Volume 39, Issue 1, 1 January 2008, Pages 127-135, ISSN 1053-8119, http://dx.doi.org/10.1016/j.neuroimage.2007.08.039.
(http://www.sciencedirect.com/science/article/pii/S1053811907007586)
Keywords: fMRI; Cortical surface; Surface-based analysis; Anatomical constraints
white_mesh: Hemisphere White Mesh ( input )white_mesh represents the mesh of the inner cortical surface, i.e. the grey / white matter interface
fmri_data: 4D Volume ( input )fmri_data is the volume to be projected on the surface. Check out that the kernels have the same size as the projected volume.
timeserie_texture: Functional Time Texture ( output )timeserie_texture is the output projected data, stored as a mesh texture.
Toolbox : Cortical Surface
User level : 0
Identifier :
CreateSurfaceBasedFunctionalDataFile name :
brainvisa/toolboxes/cortical_surface/processes/functional/CreateSurfaceBasedFunctionalData.pySupported file formats :
white_mesh :TRI mesh, Z compressed TRI mesh, PLY mesh, gz compressed TRI mesh, MESH mesh, Z compressed MESH mesh, gz compressed MESH mesh, gz compressed PLY mesh, Z compressed PLY mesh, GIFTI file, Z compressed GIFTI file, MNI OBJ mesh, gz compressed GIFTI file, Z compressed MNI OBJ mesh, gz compressed MNI OBJ meshfmri_data :GIS image, Z compressed GIS image, gz compressed GIS image, VIDA image, NIFTI-1 image, gz compressed ECAT i image, MINC image, gz compressed MINC image, TIFF image, XBM image, PBM image, PGM image, BMP image, XPM image, PPM image, gz compressed NIFTI-1 image, TIFF(.tif) image, gz compressed VIDA image, Z compressed VIDA image, Z compressed ECAT i image, gz compressed ECAT v image, ECAT i image, Z compressed ECAT v image, PNG image, JPEG image, MNG image, GIF image, Z compressed SPM image, SPM image, gz compressed SPM image, ECAT v imagetimeserie_texture :Texture