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Bold_spatial_preprocessing2 pipeline

An example of fMRI data pre-processing

Pipeline insight

spatial preprocessing2 pipeline

Inputs parameters

  • anat_file (an existing uncompressed file):

    An anatomical image (valid extensions: [.nii]). Ex. 3D T1 sequence sush as T1 turbo field echo.

    ex. /home/username/data/raw_data/Anat.nii
    
  • func_files (A list of items which are an existing uncompressed file)

    Functional images (valid extensions: [.nii]). Ex. 4D T2* sequence sush as echo planar imaging.

    ex. ['/home/username/data/raw_data/Func.nii']
    

Outputs parameters:

  • normalized_anat (a list of items which are a pathlike object or string representing a file):

    The final normalised anatomical image.

    ex. /home/username/data/derived_data/wAnat.nii
    
  • realignment_parameters (a list of items which are a pathlike object or string representing a file)

    The estimated translation and rotation parameters during the realign stage.

    ex. /home/username/data/derived_data/rp_Func.txt
    
  • smoothed_func (a list of items which are a file name)

    The final, realigned then coregistered then normalised then smoothed, functional images.

    ex. /home/username/data/derived_data/swrFunc.nii