From ab808562131e2a6f619f7ae1c06bcb0bd4546c24 Mon Sep 17 00:00:00 2001 From: clarkenj Date: Mon, 19 Feb 2024 12:41:01 -0500 Subject: [PATCH] updated README.md --- adni/README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/adni/README.md b/adni/README.md index cff7712..e04442e 100644 --- a/adni/README.md +++ b/adni/README.md @@ -7,21 +7,21 @@ Scripts for preprocessing ADNI data with fMRIPrep2.2.7lts. Data not openly available. Used BIDS-ified dataset on Elm. ## BIDS validation fixes Ran the following scripts to fix errors: -1. `1_create_dataset_description.py` +- `1_create_dataset_description.py` - creates `dataset_description.json` at the root directory with minimal information - BIDS version used is unknown, so specified latest version (see [discussion]( https://neurostars.org/t/what-bids-version-to-use-for-legacy-dataset/25619)) - fixes BIDS validation error `code: 57 DATASET_DESCRIPTION_JSON_MISSING` -2. `2_create_task-rest_bold.py` +- `2_create_task-rest_bold.py` - creates `task-rest_bold.json` at the root directory, detailing bold task - fixes BIDS validation error `code: 50 TASK_NAME_MUST_DEFINE` -3. `3_create_bidsignore.sh` +- `3_create_bidsignore.sh` - creates `.bidsignore` at the root and adds `*T1w_cropped.nii` to ignore these files, which are not needed - fixes BIDS validation error `code: 1 - NOT_INCLUDED` - TODO: check this also fixes error `code: 63 - SESSION_VALUE_CONTAINS_ILLEGAL_CHARACTER`, it should do -3. `4_correct_slice_timing.py` +- `4_correct_slice_timing.py` - halves the slice timing for sub-109S4594 (ses-20160502), which appears to be doubled (see [discussion](https://neurostars.org/t/help-with-bids-errors-66-and-75-in-legacy-dataset/25625)) - fixes BIDS validation error `code: 66 SLICETIMING_VALUES_GREATOR_THAN_REPETITION_TIME`