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Bold_spatial_preprocessing1 pipeline

An example of fMRI data pre-processing

Pipeline insight

• Bold_spatial_preprocessing1 pipeline combines the following bricks:

  • List_Duplicate

  • NewSegment

  • Normalize12

  • Realign

  • Coregister

  • Smooth

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Inputs parameters

• anat_file

  An anatomical image (ex. 3D T1 sequence such as T1 turbo field echo). An existing, uncompressed file (valid extensions: [.img, .nii, .hdr]).

  ex. /home/username/data/raw_data/Anat.nii
  

• func_files

  Functional images (ex. 4D T2* sequence such as echo planar imaging). A list of items which are an existing, uncompressed file (valid extensions: [.img, .nii, .hdr]).

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

Outputs parameters:

• bias_corrected_images

  The bias corrected images (a list of items which are a pathlike object or string representing an existing file).

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

• bias_field_images

  The estimated bias field (a list of items which are a pathlike object or string representing an existing file).

  ex. <undefined>
  

• native_class_images

  Native space probability maps (a list of items which are a list of items which are a pathlike object or string representing an existing file).

  ex. [['/home/username/data/derived_data/c1Anat.nii'],
       ['/home/username/data/derived_data/c2Anat.nii'],
       ['/home/username/data/derived_data/c3Anat.nii'],
       ['/home/username/data/derived_data/c4Anat.nii'],
       ['/home/username/data/derived_data/c5Anat.nii']]
  

• forward_deformation_field

  Forward deformation field. Could be used for spatially normalising images to MNI space (a list of items which are a pathlike object or string representing an existing file).

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

• realignment_parameters

  The estimated translation and rotation parameters during the realign stage (a list of items which are a pathlike object or string representing an existing file).

  ex. /home/username/data/derived_data/rp_Func.txt
  

• normalized_anat

  The final normalised anatomical image (a list of items which are a pathlike object or string representing an existing file).

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

• smoothed_func

  The final, realigned then registered with the anatomical image, then normalised then smoothed, functional images (a list of items which are an existing file name).

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

• coregistered_source

  Coregistered source files, corresponding to source images (a list of items which are an existing file name).

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

• normalized_func

  Functional images, realigned, registered with the anatomical image and normalized (a list of items which are an existing file name).

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