Utilities
Aux Tools
description of Aux Tools
def check_if_fem_exist(output_folder):
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This function checks if the output_folder is an existing directory or not, if the FEM exists, and if the Mesh File exists. If the output folder doesn't exist, it creates a new directory for the output_folder. Based on the existence of the FEM and Mesh file, the function produces a boolean for each variable. If the FEM and or Mesh file doesn't exist, the function returns a false boolean for each variable.
Arguments:
output_folder: path to the output folder to store the results and FEM, if it doesn't exist, it will be created.
Returns:
bool_fem_dir: a binary variable, having two possible values called “true” and “false.” If the FEM exists, the value is true. If the FEM doesn't exist, the value is false.
bool_fem_file: a binary variable, having two possible values called “true” and “false.” If the Mesh file exists, the value is true. If the mesh file doesn't exist, the value is false.
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return bool_fem_dir and bool_fem_file
def get_ids(path_mri_processed_data):
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From the provided path to processed MRI data, the function creates variables indicating the subject ID and visit.
Arguments:
path_mri_processed_data: path to processed MRI data
Returns:
subjectID: name of the subject
visit: session name
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return subjectID, visit
def mni2native(subjectID,XYZ_atlas,full_path_to_simnibs_container,path_to_fem,path_to_this_code,output_folder):
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This function takes the XYZ coordinates in atlas space, saves it in a csv file and uses it to convert the coordinates into native space using each participant's FEM. The function creates the output folder for the given coordinate in Native space.
Arguments:
subjectID: name of subject
XYZ_atlas: coordinate of vertex in atlas space in X Y Z format
full_path_to_simnibs_container: full path to the simnibs container
path_to_fem: structure of path to access each participants FEM
path_to_this_code:
output_folder: path to the output folder to store the results
Returns:
XYZ_native: coordinate of vertex in native space in X Y Z format
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return XYZ_native
def get_coord_from_csv_file(csv_file):
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This function takes a csv file and formats it into an array.
Arguments:
csv_file: The CSV (Comma-Separated Values) file format contains structured information that is separated. This file stores a desired coordinate.
Returns:
XYZ_array: Arrays are used to store multiple values in one single variable. This
array stores the coordinate of vertex in native space
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return XYZ_array
def write_coord_to_csv_file(coordinate_csv_file_name,XYZ_array):
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This function takes the coordinate array and writes it into a csv file. This csv is in the format needed for simnibs.
Arguments:
coordinate_csv_file_name: creates a csv file named after the desired
coordinate containing the coordinate in a format that is accepted by simnibs.
XYZ_array: Arrays are used to store multiple values in one single variable. This
array stores the coordinate of vertex in native space
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Cifti to Volume (Atlas and Native)
- Description : Map the content of a cifti file (dscalars, pscalars, dlabels) into a volume file (yes, no white matter) in both atlas space and in native space. White matter would be filled with NaN's. (check if nifti accept NaN's) This convertion includes cortical and subcortical structures
- Input
- Mandatory
- Cifti file , File that contain the values to be mapped into the volume.
- Cortical ribbons (pial and white matter, left and right)
- Subject Volume reference (can be native or atlas, but same as used in the cifti file used as input)
- Optional
- Atlas to native transformation matrix
- Outputs : Output volume in same space
Volume to Cifti (Atlas and Native)
- Description
- Input
- Output