<commit_before>Aligner
=======
<commit_msg>added some initial documentation on the Aligner module.<commit_after>Aligner
=======
This module contains functions for manual and automatic alignment of brain images and cortical surfaces. For each transform, it saves a transform matrix, which maps pixels to voxels.

The automatic() function does epi-to-anat registration using FLIRT with BBR, then inverts this with Transform.from_fsl()
{'fraction_non_alphanumeric': 0.0763888888888889, 'fraction_numerical': 0.0, 'mean_word_length': 6.098360655737705, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2075474', 'n_tokens_mistral': 109, 'n_tokens_neox': 101, 'n_words': 52}