diff --git a/cubids/cli.py b/cubids/cli.py index cf48cf9a..6fe7ef8d 100644 --- a/cubids/cli.py +++ b/cubids/cli.py @@ -578,7 +578,12 @@ def _parse_purge(): "scans", type=IsFile, action="store", - help="path to the txt file of scans whose associations should be purged.", + help=( + "path to the txt file of scans whose associations should be purged. " + "When specifying files in this txt file, " + "always use relative paths starting from your BIDS directory. " + "e.g., ``sub-01/ses-01/func/sub-01_ses-01_task-rest_bold.nii.gz``" + ), ) parser.add_argument( "--use-datalad", diff --git a/cubids/cubids.py b/cubids/cubids.py index 81781596..286ca0b3 100644 --- a/cubids/cubids.py +++ b/cubids/cubids.py @@ -726,7 +726,7 @@ def purge(self, scans_txt): scans_txt : str path to the .txt file that lists the scans you want to be deleted from the dataset, along - with thier associations. + with their associations. example path: /Users/Covitz/CCNP/scans_to_delete.txt """ self.scans_txt = scans_txt diff --git a/docs/example.rst b/docs/example.rst index 0f50ca80..48874ad7 100644 --- a/docs/example.rst +++ b/docs/example.rst @@ -211,13 +211,15 @@ 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, +always use relative paths starting from your BIDS directory. For this example, we created the following file: .. code-block:: console $ cat no_ped.txt - /AN/EXAMPLE/PATH/CuBIDS_Test/BIDS_Dataset_Datalad/sub-02/ses-phdiff/func/sub-02_ses-phdiff_task-rest_bold.nii.gz + sub-02/ses-phdiff/func/sub-02_ses-phdiff_task-rest_bold.nii.gz and saved it in our ``CuBIDS_Test directory``.