EstimateConstrast brick¶
Estimate contrasts of interest (SPM12 fMRI contrast manager)¶
- To define a new T-contrast:
add the contrast name in ‘T_contrast_names’ parameter
add the name of the conditions used for this contrast in ‘T_condition_names’ parameter
add the contrast weight for this contrast in ‘T_contrast_weights’ parameters
if some session should not be include, specify this in ‘session’ parameter
- To define a new F-contrast:
define the T-contrasts that should be used for estimate this F-contrast
add the contrast name in ‘F_contrast_names’ parameter
add the names of T-contrasts that should be used in ‘F_contrast_T_names’ parameter
Mandatory inputs parameters:
- spm_mat_file (a string representing an existing file):
The SPM.mat file that contains the estimate model.
ex. '/home/username/data/derived_data/SPM.mat'
- out_dir_name
Out directory name (a string, default is “stats”). It will be used only if the SPM.mat file is not already in “project/data/derived_data/subjectName_data” (for example, an SPM.mat file added in the database with the import or download button). This directory will be created in a the folder “project/data/derived_data/subjectName_data”.
:
ex. “stats”
- beta_images (a list of items which are a pathlike object or string representing an existing file)
Estimated regression coefficients.
ex. ['/home/username/data/derived_data/beta_0001.nii', '/home/username/data/derived_data/beta_0002.nii', '/home/username/data/derived_data/beta_0003.nii', '/home/username/data/derived_data/beta_0004.nii', '/home/username/data/derived_data/beta_0005.nii', '/home/username/data/derived_data/beta_0006.nii', '/home/username/data/derived_data/beta_0007.nii', '/home/username/data/derived_data/beta_0008.nii']
- residual_image (a string representing an existing file):
Mean-squared image of the residuals.
ex. '/home/username/data/derived_data/ResMS.nii'
Optional inputs parameters with a default value:
- T_contrast_names (a list of string, optional, default value is [‘+’]):
Names of each T-contrast.
ex. ['Task vs control', 'Task vs baseline']
- T_condition_names (a list of list of string, optional, default value is [[‘R1_1’]]):
Names of conditions used for each T-contrast.
ex. [['T', 'C'], ['T', 'B']]
- T_contrast_weights (a list of list of float, optional, default value is [[1.0]]):
List of contrast weights for each T-contrast.
ex. [[1, -1], [1 -1]]
- use_derivs (a boolean, optional, default value is False):
Use derivatives for estimation. Mutually exclusive group_contrast parameter.
ex. True
- group_contrast (a boolean, optional, default value is False):
Higher level contrast. Mutually exclusive use_derivs parameter.
ex. True
Optional inputs:
- session (a list of list of float, optional):
Session list. Length should be equal to the number of sessions, with 1. for sessions to include and 0. elsewhere Default is Undefined.
ex. ['0', '1.0']
- F_contrast_name (a list of string, optional):
Names of each F contrast.
ex. ['Positif effect of condition']
- F_contrast_T_names (a list of list of string, optional):
Names of T contrast used for each F contrast.
ex. [['Task vs control', 'Task vs baseline']]
Outputs parameters:
- out_spm_mat_file (a pathlike object or string representing a file):
The SPM.mat file containing specification of the design, estimated model parameters and contrast. Note that the input smp_mat_file will be overwritten.
ex. '/home/username/data/derived_data/SPM.mat'
- con_images (a list of items which are a pathlike object or string representing a file, optional):
Contrast images from a T-contrast.
ex. ['/home/username/data/derived_data/con_0001.nii', '/home/username/data/derived_data/con_0002.nii', '/home/username/data/derived_data/con_0003.nii', '/home/username/data/derived_data/con_0004.nii']
- spmT_images (a list of items which are a pathlike object or string representing a file, optional):
Stat images from a T-contrast.
ex. ['/home/username/data/derived_data/spmT_0001.nii', '/home/username/data/derived_data/spmT_0002.nii', '/home/username/data/derived_data/spmT_0003.nii', '/home/username/data/derived_data/spmT_0004.nii']
- ess_images (a list of items which are a pathlike object or string representing a file, optional):
Contrast images from a F-contrast.
ex. ['/home/username/data/derived_data/ess_0001.nii', '/home/username/data/derived_data/ess_0002.nii', '/home/username/data/derived_data/ess_0003.nii', '/home/username/data/derived_data/ess_0004.nii']
- spmF_images (a list of items which are a pathlike object or string representing a file, optional):
Stat images from a F-contrast.
ex. ['/home/username/data/derived_data/spmF_0001.nii', '/home/username/data/derived_data/spmF_0002.nii', '/home/username/data/derived_data/spmF_0003.nii', '/home/username/data/derived_data/spmF_0004.nii']
Useful links: