diff --git a/cubids/cubids.py b/cubids/cubids.py index a6c288c1..7059d639 100644 --- a/cubids/cubids.py +++ b/cubids/cubids.py @@ -709,11 +709,11 @@ def copy_exemplars(self, exemplars_dir, exemplars_tsv, min_group_size): ---------- exemplars_dir : :obj:`str` path to the directory that will contain one subject - from each Acqusition Group (*_AcqGrouping.tsv) + from each Acquisition Group (*_AcqGrouping.tsv) example path: /Users/Covitz/tsvs/CCNP_Acq_Groups/ exemplars_tsv : :obj:`str` path to the .tsv file that lists one subject - from each Acqusition Group (*_AcqGrouping.tsv + from each Acquisition Group (*_AcqGrouping.tsv from the cubids-group output) example path: /Users/Covitz/tsvs/CCNP_Acq_Grouping.tsv min_group_size : :obj:`int` @@ -923,7 +923,7 @@ def get_nifti_associations(self, nifti): A list of paths to files associated with the given NIfTI file, excluding the NIfTI file itself. """ - # get all assocation files of a nifti image + # get all association files of a nifti image no_ext_file = str(nifti).split("/")[-1].split(".")[0] associations = [] for path in Path(self.path).rglob(f"sub-*/**/{no_ext_file}.*"): diff --git a/cubids/workflows.py b/cubids/workflows.py index c85dca2f..ca531af7 100644 --- a/cubids/workflows.py +++ b/cubids/workflows.py @@ -396,7 +396,7 @@ def copy_exemplars( if use_datalad: if not bod.is_datalad_clean(): raise Exception( - "Untracked changes. Need to save " + str(bids_dir) + " before coyping exemplars" + "Untracked changes. Need to save " + str(bids_dir) + " before copying exemplars" ) bod.copy_exemplars( str(exemplars_dir), diff --git a/docs/example.rst b/docs/example.rst index b6370f4b..190bb206 100644 --- a/docs/example.rst +++ b/docs/example.rst @@ -185,8 +185,8 @@ BIDS validation but can be slowed down by extremely large datasets. .. warning:: - For internetless use cases, please see dedicated section of the `Installation page - `_ on how to download a local version + For internetless use cases, please see dedicated section of the `Installation page + `_ on how to download a local version of the validator. After that, you will need to add ``--local-validator`` option to the command string above. @@ -216,7 +216,7 @@ To do this, we run the ``cubids purge`` command. ``cubids purge`` requires as input a list of files to cleanly "purge" from the dataset. You can create this file in any text editor, as long as it is saved as plain text ``.txt``. -When specifying files in this text file, +When specifying files in this text file, always use relative paths starting from your BIDS directory. For this example, we created the following file: @@ -321,7 +321,7 @@ based on acquisition fields such as dimension and voxel sizes, number of volumes While ``v0_validation.tsv`` identified all the BIDS validation errors present in the dataset, it did not identify any potential issues that might be present within the sidecars' metadata. -Below, we see insances of missing metadata fields in a handful of sidecars, +Below, we see instances of missing metadata fields in a handful of sidecars, which may impact successful execution of BIDS Apps. .. csv-table:: v0_summary.tsv