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SliceTiming brick

Bring back every slice of a BOLD image to the reference slice time.

Inputs parameters:

  • in_files <=> scans [1]

    Path of the scans for processing (a list of items which are uncompressed files; valid extensions : [.nii]). The same parameters specified below will be applied to all data in the in_files parameter. The user will therefore make sure that all data in in_files are compatible (there is currently no verification).

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

    Type of the acquisition, either sequential ascending, sequential descending, interleaved (middle-top), interleaved (bottom-up) or interleaved (top-down). Slice ordering is assumed to be from foot to head and bottom slice = 1.

    ex. sequential ascending
  • num_slices <=> nslices [1]

    Number of slices per volume (an integer). If this parameter is undefined at the initialisation time, its value is looked in the database.

    ex. 53
  • TR <=> tr [1]

    Repetition time (a float, in seconds). This is the time between volume acquisitions. If this parameter is undefined at the initialisation time, its value is retrieved from the database.

    ex. 3.000002
  • TA <=> ta [1]

    Time of volume acquisition (a float, in seconds). If this parameter is undefined at the initialisation time, its value is automatically calculated as TR-(TR/num_slices). Must be set to 0 for the slice_order and ref_slice parameters to be automatically calculated in units of time (ms).

    ex. 2.9433981886792453
  • slice_order <=> so [1]

    Time of volume acquisition (a float, in seconds). If this parameter is undefined at the initialisation time, its value is automatically calculated as TR-(TR/num_slices). Must be set to 0 for the slice_order and ref_slice parameters to be automatically calculated in units of time (ms).

    ex. [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]
  • ref_slice <=> refslice [1]

    The chosen reference slice (an integer or a float or an _Undefined or None). It will be used as a time reference to correct the differences in the acquisition time of the slices. According to the acquisition parameter value, ref_slice is initialised to num_slices/2 (acquisition == sequential ascending or acquisition == sequential descending) or 1 (other value of acquisition). If TA is set to 0 then ref_slice will be automatically set in ms, otherwise ref_slice will be automatically calculated in slice index.

    ex. 27
  • out_prefix <=> prefix [1]

    Prefix of the output image (a string).

    ex. a

Outputs parameters:

  • timed_files

    The image after the SliceTiming correction (a pathlike object or string representing a file).

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