From 2cc6d070bb62accce5cab01734ad3488327825e8 Mon Sep 17 00:00:00 2001 From: Alberto Lazari Date: Fri, 19 Apr 2019 15:28:21 +0100 Subject: [PATCH] Made clearer names for "ds-01/2/3/4" folders; pipeline names in derivative folder; markdown file to introduce the Examples branch --- examples/BEP001_examples.md | 21 ++++++++++++++++++ .../dataset_description.json | 2 +- .../qsm_pipeline}/sub-01/anat/sub-01_QSM.json | 0 .../sub-01/anat/sub-01_QSM.nii.gz | 0 .../sub-01/anat/sub-01_T2starmap.json | 0 .../sub-01/anat/sub-01_T2starmap.nii.gz | 0 .../sub-01/anat/sub-01_FLASH.json | 0 .../sub-01/anat/sub-01_echo-1_FLASH.json | 0 .../anat/sub-01_echo-1_part-mag_FLASH.nii.gz | 0 .../sub-01_echo-1_part-phase_FLASH.nii.gz | 0 .../sub-01/anat/sub-01_echo-2_FLASH.json | 0 .../anat/sub-01_echo-2_part-mag_FLASH.nii.gz | 0 .../sub-01_echo-2_part-phase_FLASH.nii.gz | 0 .../sub-01/anat/sub-01_echo-3_FLASH.json | 0 .../anat/sub-01_echo-3_part-mag_FLASH.nii.gz | 0 .../sub-01_echo-3_part-phase_FLASH.nii.gz | 0 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.../sub-01_echo-2_part-phase_B0map.nii.gz | Bin 125 files changed, 22 insertions(+), 1 deletion(-) create mode 100644 examples/BEP001_examples.md rename examples/{ds-01 => MEGRE_multiecho}/dataset_description.json (84%) rename examples/{ds-01/derivatives => MEGRE_multiecho/derivatives/qsm_pipeline}/sub-01/anat/sub-01_QSM.json (100%) rename examples/{ds-01/derivatives => MEGRE_multiecho/derivatives/qsm_pipeline}/sub-01/anat/sub-01_QSM.nii.gz (100%) rename examples/{ds-01/derivatives => MEGRE_multiecho/derivatives/qsm_pipeline}/sub-01/anat/sub-01_T2starmap.json (100%) rename examples/{ds-01/derivatives => MEGRE_multiecho/derivatives/qsm_pipeline}/sub-01/anat/sub-01_T2starmap.nii.gz (100%) rename examples/{ds-01 => MEGRE_multiecho}/sub-01/anat/sub-01_FLASH.json (100%) rename examples/{ds-01 => MEGRE_multiecho}/sub-01/anat/sub-01_echo-1_FLASH.json (100%) rename examples/{ds-01 => MEGRE_multiecho}/sub-01/anat/sub-01_echo-1_part-mag_FLASH.nii.gz (100%) rename examples/{ds-01 => 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MPM}/sub-01/fmap/sub-01_echo-2_part-phase_B0map.json (100%) rename examples/{ds-04 => MPM}/sub-01/fmap/sub-01_echo-2_part-phase_B0map.nii.gz (100%) diff --git a/examples/BEP001_examples.md b/examples/BEP001_examples.md new file mode 100644 index 0000000..528b6a5 --- /dev/null +++ b/examples/BEP001_examples.md @@ -0,0 +1,21 @@ +# BEP001 examples + +This branch of the BEP001 repository contains some practical examples of what a BIDS-compatible qMRI dataset will look like. + +You can find more about the BEP001 addition to the BIDS standard, and the rationale for the additions/changes that it brings to the BIDS format, here: https://github.com/bids-standard/bep001. + + *The datasets in this branch contain empty data files, which might be useful for building simple software tests. + The current branch may eventually be merged with the bids-examples branch of the main bids-standard repo: https://github.com/bids-standard/bids-examples, in which case this disclaimer will be redundant.* + + +## Example 1: MEGRE, multi-echo +This is a sample dataset from a single MEGRE sequence, which yields multiple images, corresponding to different echo times. This dataset has been used to calculate a quantitative susceptibility map (QSM), as well as a T2* map. + +## Example 2: MP2RAGE, single echo +This is a sample dataset from a standard MP2RAGE sequence, which includes two GRE images acquired after a single inversion pulse. This data have been used to create a T1-map, as well as a T1-weighted image, corrected for B0 and B1-inhomogeneities, which are both part of the example dataset. + +## Example 3: MP2RAGE, multi-echo +This is a sample dataset from an MP2RAGE sequence with two inversion times, and, for the second inversion time, 4 different echoes. + +## Example 4: MultiParameter Mapping (MPM) dataset +This is a sample dataset from a MultiParameter Mapping (MPM) sequence (as per Weiskopf et al., 2013), which yields multi-echo FLASH scans that are predominantly T1-, PD-, or MT-weighted by changing repetition time and flip angle. \ No newline at end of file diff --git a/examples/ds-01/dataset_description.json b/examples/MEGRE_multiecho/dataset_description.json similarity index 84% rename from examples/ds-01/dataset_description.json rename to examples/MEGRE_multiecho/dataset_description.json index a6b88d7..7baebeb 100644 --- a/examples/ds-01/dataset_description.json +++ b/examples/MEGRE_multiecho/dataset_description.json @@ -5,5 +5,5 @@ "Kirstie Whitaker", "Gilles de Hollander" ], - "Description": "This virtual dataset is collected using a single FLASH sequence, which yields multiple images, corresponding to different echo times. This data has been used to calculate a quantitative susceptibility map, as well as a T2* map." + "Description": "This virtual dataset is collected using a single MEGRE sequence, which yields multiple images, corresponding to different echo times. This data has been used to calculate a quantitative susceptibility map, as well as a T2* map." } diff --git a/examples/ds-01/derivatives/sub-01/anat/sub-01_QSM.json b/examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_QSM.json similarity index 100% rename from examples/ds-01/derivatives/sub-01/anat/sub-01_QSM.json rename to examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_QSM.json diff --git a/examples/ds-01/derivatives/sub-01/anat/sub-01_QSM.nii.gz b/examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_QSM.nii.gz similarity index 100% rename from examples/ds-01/derivatives/sub-01/anat/sub-01_QSM.nii.gz rename to examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_QSM.nii.gz diff --git a/examples/ds-01/derivatives/sub-01/anat/sub-01_T2starmap.json b/examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_T2starmap.json similarity index 100% rename from examples/ds-01/derivatives/sub-01/anat/sub-01_T2starmap.json rename to examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_T2starmap.json diff --git a/examples/ds-01/derivatives/sub-01/anat/sub-01_T2starmap.nii.gz b/examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_T2starmap.nii.gz similarity index 100% rename from examples/ds-01/derivatives/sub-01/anat/sub-01_T2starmap.nii.gz rename to examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_T2starmap.nii.gz diff --git a/examples/ds-01/sub-01/anat/sub-01_FLASH.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_FLASH.json similarity index 100% rename from examples/ds-01/sub-01/anat/sub-01_FLASH.json rename to examples/MEGRE_multiecho/sub-01/anat/sub-01_FLASH.json diff --git a/examples/ds-01/sub-01/anat/sub-01_echo-1_FLASH.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_FLASH.json similarity index 100% rename from examples/ds-01/sub-01/anat/sub-01_echo-1_FLASH.json rename to examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_FLASH.json diff --git a/examples/ds-01/sub-01/anat/sub-01_echo-1_part-mag_FLASH.nii.gz b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_part-mag_FLASH.nii.gz similarity index 100% rename from examples/ds-01/sub-01/anat/sub-01_echo-1_part-mag_FLASH.nii.gz rename to examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_part-mag_FLASH.nii.gz diff --git a/examples/ds-01/sub-01/anat/sub-01_echo-1_part-phase_FLASH.nii.gz b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_part-phase_FLASH.nii.gz similarity index 100% rename from examples/ds-01/sub-01/anat/sub-01_echo-1_part-phase_FLASH.nii.gz rename to examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_part-phase_FLASH.nii.gz diff --git a/examples/ds-01/sub-01/anat/sub-01_echo-2_FLASH.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_FLASH.json similarity index 100% rename from examples/ds-01/sub-01/anat/sub-01_echo-2_FLASH.json rename to 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a/examples/ds-03/derivatives/sub-01/anat/sub-01_T1map.json b/examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.json similarity index 100% rename from examples/ds-03/derivatives/sub-01/anat/sub-01_T1map.json rename to examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.json diff --git a/examples/ds-02/derivatives/sub-01/anat/sub-01_T1map.nii.gz b/examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.nii.gz similarity index 100% rename from examples/ds-02/derivatives/sub-01/anat/sub-01_T1map.nii.gz rename to examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.nii.gz diff --git a/examples/ds-03/derivatives/sub-01/anat/sub-01_T2starmap.json b/examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T2starmap.json similarity index 100% rename from examples/ds-03/derivatives/sub-01/anat/sub-01_T2starmap.json rename to examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T2starmap.json diff 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