From bb6ff33e54f27bfca99222d3f86da98d31218fd2 Mon Sep 17 00:00:00 2001 From: Ashley Stewart Date: Thu, 12 Feb 2026 12:05:02 +1000 Subject: [PATCH] Add SWI example dataset Add example dataset demonstrating susceptibility weighted imaging (SWI) with MEGRE raw data and SWI, minIP and Chimap derivatives. --- dataset_listing.tsv | 1 + swi/README | 6 ++++++ swi/dataset_description.json | 8 ++++++++ swi/derivatives/swi-pipeline/README | 0 .../swi-pipeline/dataset_description.json | 15 +++++++++++++++ .../swi-pipeline/sub-01/anat/sub-01_Chimap.json | 9 +++++++++ .../swi-pipeline/sub-01/anat/sub-01_Chimap.nii.gz | 0 .../swi-pipeline/sub-01/anat/sub-01_minIP.json | 6 ++++++ .../swi-pipeline/sub-01/anat/sub-01_minIP.nii.gz | 0 .../swi-pipeline/sub-01/anat/sub-01_swi.json | 9 +++++++++ .../swi-pipeline/sub-01/anat/sub-01_swi.nii.gz | 0 .../anat/sub-01_echo-01_part-mag_MEGRE.json | 11 +++++++++++ .../anat/sub-01_echo-01_part-mag_MEGRE.nii.gz | 0 .../anat/sub-01_echo-01_part-phase_MEGRE.json | 12 ++++++++++++ .../anat/sub-01_echo-01_part-phase_MEGRE.nii.gz | 0 .../anat/sub-01_echo-02_part-mag_MEGRE.json | 11 +++++++++++ .../anat/sub-01_echo-02_part-mag_MEGRE.nii.gz | 0 .../anat/sub-01_echo-02_part-phase_MEGRE.json | 12 ++++++++++++ .../anat/sub-01_echo-02_part-phase_MEGRE.nii.gz | 0 19 files changed, 100 insertions(+) create mode 100644 swi/README create mode 100644 swi/dataset_description.json create mode 100644 swi/derivatives/swi-pipeline/README create mode 100644 swi/derivatives/swi-pipeline/dataset_description.json create mode 100644 swi/derivatives/swi-pipeline/sub-01/anat/sub-01_Chimap.json create mode 100644 swi/derivatives/swi-pipeline/sub-01/anat/sub-01_Chimap.nii.gz create mode 100644 swi/derivatives/swi-pipeline/sub-01/anat/sub-01_minIP.json create mode 100644 swi/derivatives/swi-pipeline/sub-01/anat/sub-01_minIP.nii.gz create mode 100644 swi/derivatives/swi-pipeline/sub-01/anat/sub-01_swi.json create mode 100644 swi/derivatives/swi-pipeline/sub-01/anat/sub-01_swi.nii.gz create mode 100644 swi/sub-01/anat/sub-01_echo-01_part-mag_MEGRE.json create mode 100644 swi/sub-01/anat/sub-01_echo-01_part-mag_MEGRE.nii.gz create mode 100644 swi/sub-01/anat/sub-01_echo-01_part-phase_MEGRE.json create mode 100644 swi/sub-01/anat/sub-01_echo-01_part-phase_MEGRE.nii.gz create mode 100644 swi/sub-01/anat/sub-01_echo-02_part-mag_MEGRE.json create mode 100644 swi/sub-01/anat/sub-01_echo-02_part-mag_MEGRE.nii.gz create mode 100644 swi/sub-01/anat/sub-01_echo-02_part-phase_MEGRE.json create mode 100644 swi/sub-01/anat/sub-01_echo-02_part-phase_MEGRE.nii.gz diff --git a/dataset_listing.tsv b/dataset_listing.tsv index cf5e35317..06b8fdeed 100644 --- a/dataset_listing.tsv +++ b/dataset_listing.tsv @@ -105,4 +105,5 @@ atlas-AAL n/a n/a atlas-DiFuMo n/a n/a eyetracking_fmri anat, fmap, func T1w, T2w, bold, epi, events, fieldmap, magnitude, physio atlas-suit n/a T1w +swi Example SWI dataset with MEGRE raw data and SWI, minIP and Chimap derivatives `not publicly available` anat MEGRE, swi, minIP, Chimap atlas-Juelich n/a n/a diff --git a/swi/README b/swi/README new file mode 100644 index 000000000..3ea324e51 --- /dev/null +++ b/swi/README @@ -0,0 +1,6 @@ +Example SWI dataset + +This dataset demonstrates the organization of susceptibility weighted imaging +(SWI) data in BIDS. It includes multi-echo gradient-echo (MEGRE) raw data with +magnitude and phase components, and derived SWI, minimum intensity projection +(minIP), and quantitative susceptibility map (Chimap) outputs. diff --git a/swi/dataset_description.json b/swi/dataset_description.json new file mode 100644 index 000000000..e29919aee --- /dev/null +++ b/swi/dataset_description.json @@ -0,0 +1,8 @@ +{ + "Name": "Example SWI dataset", + "BIDSVersion": "1.10.1", + "DatasetType": "raw", + "ReferencesAndLinks": [ + "https://doi.org/10.1002/mrm.20198" + ] +} diff --git a/swi/derivatives/swi-pipeline/README b/swi/derivatives/swi-pipeline/README new file mode 100644 index 000000000..e69de29bb diff --git a/swi/derivatives/swi-pipeline/dataset_description.json b/swi/derivatives/swi-pipeline/dataset_description.json new file mode 100644 index 000000000..f7a396ca5 --- /dev/null +++ b/swi/derivatives/swi-pipeline/dataset_description.json @@ -0,0 +1,15 @@ +{ + "Name": "Example SWI derivatives", + "BIDSVersion": "1.10.1", + "DatasetType": "derivative", + "SourceDatasets": [ + "../../" + ], + "GeneratedBy": [ + { + "Name": "Manual", + "Description": "Manually created example SWI derivative dataset" + } + ], + "Description": "Susceptibility weighted images (SWI), minimum intensity projections (minIP), and quantitative susceptibility maps (Chimap) derived from multi-echo gradient-echo (MEGRE) data." +} diff --git a/swi/derivatives/swi-pipeline/sub-01/anat/sub-01_Chimap.json b/swi/derivatives/swi-pipeline/sub-01/anat/sub-01_Chimap.json new file mode 100644 index 000000000..bd1fb4a23 --- /dev/null +++ b/swi/derivatives/swi-pipeline/sub-01/anat/sub-01_Chimap.json @@ -0,0 +1,9 @@ +{ + "Sources": [ + "bids:raw:sub-01/anat/sub-01_echo-01_part-mag_MEGRE.nii.gz", + "bids:raw:sub-01/anat/sub-01_echo-01_part-phase_MEGRE.nii.gz", + "bids:raw:sub-01/anat/sub-01_echo-02_part-mag_MEGRE.nii.gz", + "bids:raw:sub-01/anat/sub-01_echo-02_part-phase_MEGRE.nii.gz" + ], + "MagneticFieldStrength": 3 +} diff --git a/swi/derivatives/swi-pipeline/sub-01/anat/sub-01_Chimap.nii.gz b/swi/derivatives/swi-pipeline/sub-01/anat/sub-01_Chimap.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/swi/derivatives/swi-pipeline/sub-01/anat/sub-01_minIP.json b/swi/derivatives/swi-pipeline/sub-01/anat/sub-01_minIP.json new file mode 100644 index 000000000..838152b5e --- /dev/null +++ b/swi/derivatives/swi-pipeline/sub-01/anat/sub-01_minIP.json @@ -0,0 +1,6 @@ +{ + "Sources": [ + "bids::sub-01/anat/sub-01_swi.nii.gz" + ], + "MagneticFieldStrength": 3 +} diff --git a/swi/derivatives/swi-pipeline/sub-01/anat/sub-01_minIP.nii.gz b/swi/derivatives/swi-pipeline/sub-01/anat/sub-01_minIP.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/swi/derivatives/swi-pipeline/sub-01/anat/sub-01_swi.json b/swi/derivatives/swi-pipeline/sub-01/anat/sub-01_swi.json new file mode 100644 index 000000000..bd1fb4a23 --- /dev/null +++ b/swi/derivatives/swi-pipeline/sub-01/anat/sub-01_swi.json @@ -0,0 +1,9 @@ +{ + "Sources": [ + "bids:raw:sub-01/anat/sub-01_echo-01_part-mag_MEGRE.nii.gz", + "bids:raw:sub-01/anat/sub-01_echo-01_part-phase_MEGRE.nii.gz", + "bids:raw:sub-01/anat/sub-01_echo-02_part-mag_MEGRE.nii.gz", + "bids:raw:sub-01/anat/sub-01_echo-02_part-phase_MEGRE.nii.gz" + ], + "MagneticFieldStrength": 3 +} diff --git a/swi/derivatives/swi-pipeline/sub-01/anat/sub-01_swi.nii.gz b/swi/derivatives/swi-pipeline/sub-01/anat/sub-01_swi.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/swi/sub-01/anat/sub-01_echo-01_part-mag_MEGRE.json b/swi/sub-01/anat/sub-01_echo-01_part-mag_MEGRE.json new file mode 100644 index 000000000..c40ec5670 --- /dev/null +++ b/swi/sub-01/anat/sub-01_echo-01_part-mag_MEGRE.json @@ -0,0 +1,11 @@ +{ + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturerModelName": "Prisma", + "PulseSequenceType": "GR", + "MRAcquisitionType": "3D", + "EchoTime": 0.006, + "RepetitionTimeExcitation": 0.03, + "FlipAngle": 15, + "AcquisitionVoxelSize": [0.9, 0.9, 1.5] +} diff --git a/swi/sub-01/anat/sub-01_echo-01_part-mag_MEGRE.nii.gz b/swi/sub-01/anat/sub-01_echo-01_part-mag_MEGRE.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/swi/sub-01/anat/sub-01_echo-01_part-phase_MEGRE.json b/swi/sub-01/anat/sub-01_echo-01_part-phase_MEGRE.json new file mode 100644 index 000000000..4b6b5f09b --- /dev/null +++ b/swi/sub-01/anat/sub-01_echo-01_part-phase_MEGRE.json @@ -0,0 +1,12 @@ +{ + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturerModelName": "Prisma", + "PulseSequenceType": "GR", + "MRAcquisitionType": "3D", + "EchoTime": 0.006, + "RepetitionTimeExcitation": 0.03, + "FlipAngle": 15, + "AcquisitionVoxelSize": [0.9, 0.9, 1.5], + "Units": "arbitrary" +} diff --git a/swi/sub-01/anat/sub-01_echo-01_part-phase_MEGRE.nii.gz b/swi/sub-01/anat/sub-01_echo-01_part-phase_MEGRE.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/swi/sub-01/anat/sub-01_echo-02_part-mag_MEGRE.json b/swi/sub-01/anat/sub-01_echo-02_part-mag_MEGRE.json new file mode 100644 index 000000000..99ec62711 --- /dev/null +++ b/swi/sub-01/anat/sub-01_echo-02_part-mag_MEGRE.json @@ -0,0 +1,11 @@ +{ + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturerModelName": "Prisma", + "PulseSequenceType": "GR", + "MRAcquisitionType": "3D", + "EchoTime": 0.012, + "RepetitionTimeExcitation": 0.03, + "FlipAngle": 15, + "AcquisitionVoxelSize": [0.9, 0.9, 1.5] +} diff --git a/swi/sub-01/anat/sub-01_echo-02_part-mag_MEGRE.nii.gz b/swi/sub-01/anat/sub-01_echo-02_part-mag_MEGRE.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/swi/sub-01/anat/sub-01_echo-02_part-phase_MEGRE.json b/swi/sub-01/anat/sub-01_echo-02_part-phase_MEGRE.json new file mode 100644 index 000000000..b40673370 --- /dev/null +++ b/swi/sub-01/anat/sub-01_echo-02_part-phase_MEGRE.json @@ -0,0 +1,12 @@ +{ + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturerModelName": "Prisma", + "PulseSequenceType": "GR", + "MRAcquisitionType": "3D", + "EchoTime": 0.012, + "RepetitionTimeExcitation": 0.03, + "FlipAngle": 15, + "AcquisitionVoxelSize": [0.9, 0.9, 1.5], + "Units": "arbitrary" +} diff --git a/swi/sub-01/anat/sub-01_echo-02_part-phase_MEGRE.nii.gz b/swi/sub-01/anat/sub-01_echo-02_part-phase_MEGRE.nii.gz new file mode 100644 index 000000000..e69de29bb