From 529fac85da6120694ea8df2921f7cfbc17a53a60 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 29 Oct 2022 22:04:06 +0200 Subject: [PATCH 1/4] use bids uri for mpm derivatives --- .../derivatives/hmri/dataset_description.json | 5 ++++- .../hmri/sub-01/fmap/sub-01_acq-MTw_RB1map.json | 12 ++++++------ .../hmri/sub-01/fmap/sub-01_acq-PDw_RB1map.json | 16 ++++++++-------- .../hmri/sub-01/fmap/sub-01_acq-T1w_RB1map.json | 16 ++++++++-------- 4 files changed, 26 insertions(+), 23 deletions(-) diff --git a/qmri_mpm/derivatives/hmri/dataset_description.json b/qmri_mpm/derivatives/hmri/dataset_description.json index e7d9cf745..ef89418b6 100644 --- a/qmri_mpm/derivatives/hmri/dataset_description.json +++ b/qmri_mpm/derivatives/hmri/dataset_description.json @@ -15,6 +15,9 @@ "https://doi.org/10.1016/j.dib.2019.104132", "https://doi.org/10.1016/j.neuroimage.2019.01.029", "https://doi.org/10.1016/j.dib.2019.104132" - ] + ], + "DatasetLinks": { + "source": "../../" + } } \ No newline at end of file diff --git a/qmri_mpm/derivatives/hmri/sub-01/fmap/sub-01_acq-MTw_RB1map.json b/qmri_mpm/derivatives/hmri/sub-01/fmap/sub-01_acq-MTw_RB1map.json index 68c544ced..423436272 100644 --- a/qmri_mpm/derivatives/hmri/sub-01/fmap/sub-01_acq-MTw_RB1map.json +++ b/qmri_mpm/derivatives/hmri/sub-01/fmap/sub-01_acq-MTw_RB1map.json @@ -1,11 +1,11 @@ { "IntendedFor": [ - "anat/sub-01_acq-MTw_echo-1_flip-1_mt-on_MPM.nii", - "anat/sub-01_acq-MTw_echo-2_flip-1_mt-on_MPM.nii", - "anat/sub-01_acq-MTw_echo-3_flip-1_mt-on_MPM.nii", - "anat/sub-01_acq-MTw_echo-4_flip-1_mt-on_MPM.nii", - "anat/sub-01_acq-MTw_echo-5_flip-1_mt-on_MPM.nii", - "anat/sub-01_acq-MTw_echo-6_flip-1_mt-on_MPM.nii" + "bids:source:sub-01/anat/sub-01_acq-MTw_echo-1_flip-1_mt-on_MPM.nii", + "bids:source:sub-01/anat/sub-01_acq-MTw_echo-2_flip-1_mt-on_MPM.nii", + "bids:source:sub-01/anat/sub-01_acq-MTw_echo-3_flip-1_mt-on_MPM.nii", + "bids:source:sub-01/anat/sub-01_acq-MTw_echo-4_flip-1_mt-on_MPM.nii", + "bids:source:sub-01/anat/sub-01_acq-MTw_echo-5_flip-1_mt-on_MPM.nii", + "bids:source:sub-01/anat/sub-01_acq-MTw_echo-6_flip-1_mt-on_MPM.nii" ], "RawSources": [ "sub-01/fmap/sub-01_acq-bodyMTw_RB1COR.nii", diff --git a/qmri_mpm/derivatives/hmri/sub-01/fmap/sub-01_acq-PDw_RB1map.json b/qmri_mpm/derivatives/hmri/sub-01/fmap/sub-01_acq-PDw_RB1map.json index 4d34c98b6..bc8c402c6 100644 --- a/qmri_mpm/derivatives/hmri/sub-01/fmap/sub-01_acq-PDw_RB1map.json +++ b/qmri_mpm/derivatives/hmri/sub-01/fmap/sub-01_acq-PDw_RB1map.json @@ -1,13 +1,13 @@ { "IntendedFor": [ - "anat/sub-01_acq-PDw_echo-1_flip-1_mt-off_MPM.nii", - "anat/sub-01_acq-PDw_echo-2_flip-1_mt-off_MPM.nii", - "anat/sub-01_acq-PDw_echo-3_flip-1_mt-off_MPM.nii", - "anat/sub-01_acq-PDw_echo-4_flip-1_mt-off_MPM.nii", - "anat/sub-01_acq-PDw_echo-5_flip-1_mt-off_MPM.nii", - "anat/sub-01_acq-PDw_echo-6_flip-1_mt-off_MPM.nii", - "anat/sub-01_acq-PDw_echo-7_flip-1_mt-off_MPM.nii", - "anat/sub-01_acq-PDw_echo-8_flip-1_mt-off_MPM.nii" + "bids:source:sub-01/anat/sub-01_acq-PDw_echo-1_flip-1_mt-off_MPM.nii", + "bids:source:sub-01/anat/sub-01_acq-PDw_echo-2_flip-1_mt-off_MPM.nii", + "bids:source:sub-01/anat/sub-01_acq-PDw_echo-3_flip-1_mt-off_MPM.nii", + "bids:source:sub-01/anat/sub-01_acq-PDw_echo-4_flip-1_mt-off_MPM.nii", + "bids:source:sub-01/anat/sub-01_acq-PDw_echo-5_flip-1_mt-off_MPM.nii", + "bids:source:sub-01/anat/sub-01_acq-PDw_echo-6_flip-1_mt-off_MPM.nii", + "bids:source:sub-01/anat/sub-01_acq-PDw_echo-7_flip-1_mt-off_MPM.nii", + "bids:source:sub-01/anat/sub-01_acq-PDw_echo-8_flip-1_mt-off_MPM.nii" ], "RawSources": [ "sub-01/fmap/sub-01_acq-bodyPDw_RB1COR.nii", diff --git a/qmri_mpm/derivatives/hmri/sub-01/fmap/sub-01_acq-T1w_RB1map.json b/qmri_mpm/derivatives/hmri/sub-01/fmap/sub-01_acq-T1w_RB1map.json index afae8b32b..505f637c0 100644 --- a/qmri_mpm/derivatives/hmri/sub-01/fmap/sub-01_acq-T1w_RB1map.json +++ b/qmri_mpm/derivatives/hmri/sub-01/fmap/sub-01_acq-T1w_RB1map.json @@ -1,13 +1,13 @@ { "IntendedFor": [ - "anat/sub-01_acq-T1w_echo-1_flip-2_mt-off_MPM.nii", - "anat/sub-01_acq-T1w_echo-2_flip-2_mt-off_MPM.nii", - "anat/sub-01_acq-T1w_echo-3_flip-2_mt-off_MPM.nii", - "anat/sub-01_acq-T1w_echo-4_flip-2_mt-off_MPM.nii", - "anat/sub-01_acq-T1w_echo-5_flip-2_mt-off_MPM.nii", - "anat/sub-01_acq-T1w_echo-6_flip-2_mt-off_MPM.nii", - "anat/sub-01_acq-T1w_echo-7_flip-2_mt-off_MPM.nii", - "anat/sub-01_acq-T1w_echo-8_flip-2_mt-off_MPM.nii" + "bids:source:sub-01/anat/sub-01_acq-T1w_echo-1_flip-2_mt-off_MPM.nii", + "bids:source:sub-01/anat/sub-01_acq-T1w_echo-2_flip-2_mt-off_MPM.nii", + "bids:source:sub-01/anat/sub-01_acq-T1w_echo-3_flip-2_mt-off_MPM.nii", + "bids:source:sub-01/anat/sub-01_acq-T1w_echo-4_flip-2_mt-off_MPM.nii", + "bids:source:sub-01/anat/sub-01_acq-T1w_echo-5_flip-2_mt-off_MPM.nii", + "bids:source:sub-01/anat/sub-01_acq-T1w_echo-6_flip-2_mt-off_MPM.nii", + "bids:source:sub-01/anat/sub-01_acq-T1w_echo-7_flip-2_mt-off_MPM.nii", + "bids:source:sub-01/anat/sub-01_acq-T1w_echo-8_flip-2_mt-off_MPM.nii" ], "RawSources": [ "sub-01/fmap/sub-01_acq-bodyT1w_RB1COR.nii", From ccebff477be695fa1185d7b815347236fa6513bf Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 29 Oct 2022 22:07:18 +0200 Subject: [PATCH 2/4] apply URI for other qmri datasets --- qmri_mtsat/derivatives/qMRLab/dataset_description.json | 5 ++++- qmri_mtsat/derivatives/qMRLab/sub-01/fmap/sub-01_TB1map.json | 4 ++-- qmri_vfa/derivatives/qMRLab/dataset_description.json | 5 ++++- qmri_vfa/derivatives/qMRLab/sub-01/fmap/sub-01_TB1map.json | 2 +- 4 files changed, 11 insertions(+), 5 deletions(-) diff --git a/qmri_mtsat/derivatives/qMRLab/dataset_description.json b/qmri_mtsat/derivatives/qMRLab/dataset_description.json index d8a8735e2..53525bcba 100644 --- a/qmri_mtsat/derivatives/qMRLab/dataset_description.json +++ b/qmri_mtsat/derivatives/qMRLab/dataset_description.json @@ -9,5 +9,8 @@ "Name": "Manual", "Description": "Adapted from existing example, adjusted to conform to BIDS Derivatives" } - ] + ], + "DatasetLinks": { + "source": "../../" +} } diff --git a/qmri_mtsat/derivatives/qMRLab/sub-01/fmap/sub-01_TB1map.json b/qmri_mtsat/derivatives/qMRLab/sub-01/fmap/sub-01_TB1map.json index 62d0042db..72b798b18 100644 --- a/qmri_mtsat/derivatives/qMRLab/sub-01/fmap/sub-01_TB1map.json +++ b/qmri_mtsat/derivatives/qMRLab/sub-01/fmap/sub-01_TB1map.json @@ -1,7 +1,7 @@ { "RawSources": [ - "sub-01/fmap/sub-01_flip-01_TB1DAM.nii.gz", - "sub-01/fmap/sub-01_flip-02_TB1DAM.nii.gz" + "bids:source:sub-01/sub-01/fmap/sub-01_flip-01_TB1DAM.nii.gz", + "bids:source:sub-01/sub-01/fmap/sub-01_flip-02_TB1DAM.nii.gz" ], "IntendedFor": [ "anat/sub-01_T1map.nii.gz" diff --git a/qmri_vfa/derivatives/qMRLab/dataset_description.json b/qmri_vfa/derivatives/qMRLab/dataset_description.json index 24a9cfafa..f659fe369 100644 --- a/qmri_vfa/derivatives/qMRLab/dataset_description.json +++ b/qmri_vfa/derivatives/qMRLab/dataset_description.json @@ -14,5 +14,8 @@ "Name": "Manual", "Description": "Adjusted to conform to BIDS Derivatives" } - ] + ], + "DatasetLinks": { + "source": "../../" +} } diff --git a/qmri_vfa/derivatives/qMRLab/sub-01/fmap/sub-01_TB1map.json b/qmri_vfa/derivatives/qMRLab/sub-01/fmap/sub-01_TB1map.json index 2b03b7ed8..989c4d9d3 100644 --- a/qmri_vfa/derivatives/qMRLab/sub-01/fmap/sub-01_TB1map.json +++ b/qmri_vfa/derivatives/qMRLab/sub-01/fmap/sub-01_TB1map.json @@ -3,7 +3,7 @@ "sub-01/fmap/sub-01_acq-tr2_TB1AFI.nii.gz" ], "IntendedFor": [ - "anat/sub-01_T1map.nii.gz" + "bids:source:sub-01/anat/sub-01_T1map.nii.gz" ], "MagneticFieldStrength": "3", "Manufacturer": "Siemens", From 28231df300b7090926743e810a395ac398c45152 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Tue, 8 Nov 2022 20:22:00 +0100 Subject: [PATCH 3/4] Apply suggestions from code review Co-authored-by: Stefan Appelhoff --- qmri_mpm/derivatives/hmri/dataset_description.json | 2 +- qmri_mtsat/derivatives/qMRLab/dataset_description.json | 2 +- qmri_vfa/derivatives/qMRLab/dataset_description.json | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/qmri_mpm/derivatives/hmri/dataset_description.json b/qmri_mpm/derivatives/hmri/dataset_description.json index ef89418b6..203c12861 100644 --- a/qmri_mpm/derivatives/hmri/dataset_description.json +++ b/qmri_mpm/derivatives/hmri/dataset_description.json @@ -17,7 +17,7 @@ "https://doi.org/10.1016/j.dib.2019.104132" ], "DatasetLinks": { - "source": "../../" + "source": "file://../../" } } \ No newline at end of file diff --git a/qmri_mtsat/derivatives/qMRLab/dataset_description.json b/qmri_mtsat/derivatives/qMRLab/dataset_description.json index 53525bcba..5ecb15986 100644 --- a/qmri_mtsat/derivatives/qMRLab/dataset_description.json +++ b/qmri_mtsat/derivatives/qMRLab/dataset_description.json @@ -11,6 +11,6 @@ } ], "DatasetLinks": { - "source": "../../" + "source": "file://../../" } } diff --git a/qmri_vfa/derivatives/qMRLab/dataset_description.json b/qmri_vfa/derivatives/qMRLab/dataset_description.json index f659fe369..e85095bd9 100644 --- a/qmri_vfa/derivatives/qMRLab/dataset_description.json +++ b/qmri_vfa/derivatives/qMRLab/dataset_description.json @@ -16,6 +16,6 @@ } ], "DatasetLinks": { - "source": "../../" + "source": "file://../../" } } From 6494495856044fbf08dce92a062934b59a5f7171 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Mon, 2 Jan 2023 15:49:44 +0100 Subject: [PATCH 4/4] Apply suggestions from code review Co-authored-by: Stefan Appelhoff --- qmri_mpm/derivatives/hmri/dataset_description.json | 2 +- qmri_mtsat/derivatives/qMRLab/dataset_description.json | 2 +- qmri_vfa/derivatives/qMRLab/dataset_description.json | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/qmri_mpm/derivatives/hmri/dataset_description.json b/qmri_mpm/derivatives/hmri/dataset_description.json index 203c12861..ef89418b6 100644 --- a/qmri_mpm/derivatives/hmri/dataset_description.json +++ b/qmri_mpm/derivatives/hmri/dataset_description.json @@ -17,7 +17,7 @@ "https://doi.org/10.1016/j.dib.2019.104132" ], "DatasetLinks": { - "source": "file://../../" + "source": "../../" } } \ No newline at end of file diff --git a/qmri_mtsat/derivatives/qMRLab/dataset_description.json b/qmri_mtsat/derivatives/qMRLab/dataset_description.json index 5ecb15986..53525bcba 100644 --- a/qmri_mtsat/derivatives/qMRLab/dataset_description.json +++ b/qmri_mtsat/derivatives/qMRLab/dataset_description.json @@ -11,6 +11,6 @@ } ], "DatasetLinks": { - "source": "file://../../" + "source": "../../" } } diff --git a/qmri_vfa/derivatives/qMRLab/dataset_description.json b/qmri_vfa/derivatives/qMRLab/dataset_description.json index e85095bd9..f659fe369 100644 --- a/qmri_vfa/derivatives/qMRLab/dataset_description.json +++ b/qmri_vfa/derivatives/qMRLab/dataset_description.json @@ -16,6 +16,6 @@ } ], "DatasetLinks": { - "source": "file://../../" + "source": "../../" } }