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ExtractSignalROI brick

Extract signals from ROI using a segmentation file with label

Mandatory inputs parameters:

  • in_file (a string representing an existing file)

    Input image (valid extensions: [.nii, .nii.gz]). Signals will be extracted from this image.

    ex. '/home/username/data/raw_data/sub-001_bold.nii'
    
  • in_seg (a string representing an existing file)

    Input segmented image (valid extensions: [.nii, .nii.gz]). For example a binary brain mask or an image of tissues or structures segmentation (each region should be associated to an integer).

    ex. '/home/username/data/raw_data/native_structures_sub-001_bold_space.nii'
    
  • labels (a list of integer)

    List of the labels of the ROI to extract.

    ex. ['47', '48']
    

Outputs parameters:

  • signals (a pathlike object or string representing a file)

    Extracted signal for each ROI in a csv file.

    ex. '/home/username/data/raw_data/sub-001_bold_extracted_signals_47_48.csv'
    

Useful links:

nilearn NiftiLabelsMasker