bids.reports.utils

Generate publication-quality data acquisition methods section from BIDS dataset.

Utilities to generate the MRI data acquisition portion of a methods section from a BIDS dataset.

Functions

get_seqstr(config, metadata)

Extract and reformat imaging sequence(s) and variant(s) into pretty strings.

get_sizestr(img)

Extract and reformat voxel size, matrix size, field of view, and number of slices into pretty strings.

get_slice_info(slice_times)

Extract slice order from slice timing info.

list_to_str(lst)

Turn a list into a comma- and/or and-separated string.

num_to_str(num)

Convert an int or float to a nice string.

reminder()

Remind users about things they need to do after generating the report.

remove_duplicates(seq)

Return unique elements from list while preserving order.

get_seqstr(config, metadata)[source]

Extract and reformat imaging sequence(s) and variant(s) into pretty strings.

Parameters
  • config (dict) – A dictionary with relevant information regarding sequences, sequence variants, phase encoding directions, and task names.

  • metadata (dict) – The metadata for the scan.

Returns

  • seqs (str) – Sequence names.

  • variants (str) – Sequence variant names.

get_sizestr(img)[source]

Extract and reformat voxel size, matrix size, field of view, and number of slices into pretty strings.

Parameters

img (nibabel.Nifti1Image) – Image from scan from which to derive parameters.

Returns

  • n_slices (int) – Number of slices.

  • voxel_size (str) – Voxel size string (e.g., ‘2x2x2’)

  • matrix_size (str) – Matrix size string (e.g., ‘128x128’)

  • fov (str) – Field of view string (e.g., ‘256x256’)

get_slice_info(slice_times)[source]

Extract slice order from slice timing info.

TODO: Be more specific with slice orders. Currently anything where there’s some kind of skipping is interpreted as interleaved of some kind.

Parameters

slice_times (array-like) – A list of slice times in seconds or milliseconds or whatever.

Returns

slice_order_name – The name of the slice order sequence.

Return type

str

list_to_str(lst)[source]

Turn a list into a comma- and/or and-separated string.

Parameters

lst (list) – A list of strings to join into a single string.

Returns

str_ – A string with commas and/or ands separating th elements from lst.

Return type

str

num_to_str(num)[source]

Convert an int or float to a nice string. E.g.,

21 -> ‘21’ 2.500 -> ‘2.5’ 3. -> ‘3’

reminder()[source]

Remind users about things they need to do after generating the report.

remove_duplicates(seq)[source]

Return unique elements from list while preserving order. From https://stackoverflow.com/a/480227/2589328