From 9fb0d5b074b17cda7c58ca9f3190ab3b38e5a884 Mon Sep 17 00:00:00 2001 From: Gregory Conan Date: Mon, 8 Jun 2020 11:15:42 -0700 Subject: [PATCH] Minor edits --- README.md | 2 +- abcd2bids.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 588ff4a..aaee2c9 100755 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ Written by the OHSU ABCD site for selectively downloading ABCD Study imaging DICOM data QC'ed as good by the ABCD DAIC site, converting it to BIDS standard input data, selecting the best pair of spin echo field maps, and correcting the sidecar JSON files to meet the BIDS Validator specification. -*Note: DWI has been added to the list of modalities that can be downloaded. This has resulted in a couple important changes to the scripts included here and the output BIDS data. Most notabaly fieldmaps now include an acquisition field in their filenames to differentiate those used for functional images and those used for DWI (e.g. ..._acq-func_... or ..._acq-dwi_...). Data uploaded to [Collection 3165](https://github.com/ABCD-STUDY/nda-abcd-collection-3165), which was created using this repository, does not contain this identifier.* +*Note: DWI has been added to the list of modalities that can be downloaded. This has resulted in a couple important changes to the scripts included here and the output BIDS data. Most notably, fieldmaps now include an acquisition field in their filenames to differentiate those used for functional images and those used for DWI (e.g. ..._acq-func_... or ..._acq-dwi_...). Data uploaded to [Collection 3165](https://github.com/ABCD-STUDY/nda-abcd-collection-3165), which was created using this repository, does not contain this identifier.* ## Installation diff --git a/abcd2bids.py b/abcd2bids.py index 67398f5..f6d3f5c 100755 --- a/abcd2bids.py +++ b/abcd2bids.py @@ -4,7 +4,7 @@ ABCD to BIDS CLI Wrapper Greg Conan: conan@ohsu.edu Created 2019-05-29 -Updated 2020-05-19 +Updated 2020-06-02 """ ################################## @@ -625,6 +625,7 @@ def download_nda_data(cli_args): "--modalities", ','.join(cli_args.modalities)), stdin=subprocess.PIPE) + def unpack_and_setup(cli_args): """ Run unpack_and_setup.sh script repeatedly to unpack and setup the newly