eneral tools to analyse fMRI datasets (GLM fit) sampled on the surface.
This relies massively on glm_tools, and on the tio module to perform io on (AIMS .tex) textures. This should be replaced in a near future by pygifti modules.
Author : Bertrand Thirion, 2010
Contrast computation utility
Parameters : | contrast_struct, ConfigObj instance or string :
misc: misc object instance, :
Complete_Paths: dictionary or string, :
glms, dictionary of nipy.neurospin.glm.glm.glm instances :
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This function returns a dictionary with all the paths of all the paths where something id read or written in a standard GLM. The hard-coded paths reflect brainvisa database conventions. Additionally, this creates the missing output directories.
Parameters : | base_path: string, :
sessions: list of strings :
fmri_wc: string, :
model_id: string, :
misc_id: string, optional :
paradigm_id: string, optional :
contrast_id: string, optional :
design_id: string, optional :
glm_dump: string, optional, :
glm_config: string, optional, :
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Returns : | paths, dictionary :
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This function generate standard output paths for all the contrasts and arranges them in a dictionary
Parameters : | output_dir_path: string, :
contrasts: ConfigObj instance, :
side: string, :
z_file: bool, optional :
stat_file: bool, optional :
con_file: bool, optional, :
res_file: bool, optional :
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Returns : | path, a dictiorany with all paths : |
Call the GLM Fit function with apropriate arguments
Parameters : | fMRI_path, string or list of strings, :
design_matrix, DesignMatrix instance, optional :
output_glm, string, optional :
outputCon, string,optional :
fit= ‘Kalman_AR1’, string to be chosen among :
design_marix_path: string, :
data_scaling: bool, Optional :
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Returns : | glm, a nipy.neurospin.glm.glm instance representing the GLM : |
Return an array from texture data
Parameters : | path string or list of strings :
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Returns : | data array of shape (nnode) or (nnode, len(path)) :
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idem savel_all, but the names are now all included in kargs
volume saving utility for textures
Parameters : | path, string, output image path : data, array of shape (nnode) :
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