From 31f27d852d84651953fdf4a13225f9477432d90c Mon Sep 17 00:00:00 2001 From: CPernet Date: Fri, 26 Jan 2024 09:26:09 +0100 Subject: [PATCH 1/4] propose diff folder names --- .../README | 0 .../dataset_description.json | 0 .../derivatives/atlas_pipeline/dataset_description.json | 0 .../sub-01/anat/sub-01_atlas-IndividualParc_dseg.json | 0 .../sub-01/anat/sub-01_atlas-IndividualParc_dseg.nii.gz | 0 .../sub-01/anat/sub-01_atlas-IndividualParc_dseg.tsv | 0 .../participants.json | 0 .../participants.tsv | 0 .../sub-01/anat/sub-01_T1w.json | 0 .../sub-01/anat/sub-01_T1w.nii.gz | 0 .../README | 0 .../atlas-AAL/atlas-AAL_space-MNI152NLin6Asym_res-1_dseg.json | 0 .../atlas-AAL/atlas-AAL_space-MNI152NLin6Asym_res-1_dseg.nii.gz | 0 .../atlas-AAL/atlas-AAL_space-MNI152NLin6Asym_res-1_dseg.tsv | 0 .../dataset_description.json | 0 .../derivatives/atlas_pipeline/dataset_description.json | 0 .../sub-01/anat/sub-01_space-orig_seg-AAL_dseg.json | 0 .../sub-01/anat/sub-01_space-orig_seg-AAL_dseg.nii.gz | 0 .../atlas_pipeline/sub-01/anat/sub-01_space-orig_seg-AAL_dseg.tsv | 0 .../participants.json | 0 .../participants.tsv | 0 .../sub-01/anat/sub-01_T1w.json | 0 .../sub-01/anat/sub-01_T1w.nii.gz | 0 .../README | 0 ...HarvardOxford_space-MNI152NLin6Asym_res-1_desc-Thr25_dseg.json | 0 ...rvardOxford_space-MNI152NLin6Asym_res-1_desc-Thr25_dseg.nii.gz | 0 ...-HarvardOxford_space-MNI152NLin6Asym_res-1_desc-Thr25_dseg.tsv | 0 .../dataset_description.json | 0 .../atlas-HarvardOxford_space-NKI_res-1_desc-Thr25_dseg.json | 0 .../atlas-HarvardOxford_space-NKI_res-1_desc-Thr25_dseg.nii.gz | 0 .../atlas-HarvardOxford_space-NKI_res-1_desc-Thr25_dseg.tsv | 0 .../derivatives/atlas_pipeline/dataset_description.json | 0 32 files changed, 0 insertions(+), 0 deletions(-) rename {atlas_within_dataset_derived_subject_space => atlas_derived_from_subjects_case3}/README (100%) rename {atlas_within_dataset_derived_subject_space => atlas_derived_from_subjects_case3}/dataset_description.json (100%) rename 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atlas_derived_from_subjects_case3}/sub-01/anat/sub-01_T1w.json (100%) rename {atlas_within_dataset_derived_subject_space => atlas_derived_from_subjects_case3}/sub-01/anat/sub-01_T1w.nii.gz (100%) rename {atlas_within_dataset_transformed_subject_space => atlas_transformed2subject_space_case2}/README (100%) rename {atlas_within_dataset_transformed_subject_space => atlas_transformed2subject_space_case2}/atlas/atlas-AAL/atlas-AAL_space-MNI152NLin6Asym_res-1_dseg.json (100%) rename {atlas_within_dataset_transformed_subject_space => atlas_transformed2subject_space_case2}/atlas/atlas-AAL/atlas-AAL_space-MNI152NLin6Asym_res-1_dseg.nii.gz (100%) rename {atlas_within_dataset_transformed_subject_space => atlas_transformed2subject_space_case2}/atlas/atlas-AAL/atlas-AAL_space-MNI152NLin6Asym_res-1_dseg.tsv (100%) rename {atlas_within_dataset_transformed_subject_space => atlas_transformed2subject_space_case2}/dataset_description.json (100%) rename {atlas_within_dataset_transformed_subject_space => atlas_transformed2subject_space_case2}/derivatives/atlas_pipeline/dataset_description.json (100%) rename {atlas_within_dataset_transformed_subject_space => atlas_transformed2subject_space_case2}/derivatives/atlas_pipeline/sub-01/anat/sub-01_space-orig_seg-AAL_dseg.json (100%) rename {atlas_within_dataset_transformed_subject_space => atlas_transformed2subject_space_case2}/derivatives/atlas_pipeline/sub-01/anat/sub-01_space-orig_seg-AAL_dseg.nii.gz (100%) rename {atlas_within_dataset_transformed_subject_space => atlas_transformed2subject_space_case2}/derivatives/atlas_pipeline/sub-01/anat/sub-01_space-orig_seg-AAL_dseg.tsv (100%) rename {atlas_within_dataset_transformed_subject_space => atlas_transformed2subject_space_case2}/participants.json (100%) rename {atlas_within_dataset_transformed_subject_space => atlas_transformed2subject_space_case2}/participants.tsv (100%) rename {atlas_within_dataset_transformed_subject_space => 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a/atlas_within_dataset_transformed_subject_space/derivatives/atlas_pipeline/dataset_description.json b/atlas_transformed2subject_space_case2/derivatives/atlas_pipeline/dataset_description.json similarity index 100% rename from atlas_within_dataset_transformed_subject_space/derivatives/atlas_pipeline/dataset_description.json rename to atlas_transformed2subject_space_case2/derivatives/atlas_pipeline/dataset_description.json diff --git a/atlas_within_dataset_transformed_subject_space/derivatives/atlas_pipeline/sub-01/anat/sub-01_space-orig_seg-AAL_dseg.json b/atlas_transformed2subject_space_case2/derivatives/atlas_pipeline/sub-01/anat/sub-01_space-orig_seg-AAL_dseg.json similarity index 100% rename from atlas_within_dataset_transformed_subject_space/derivatives/atlas_pipeline/sub-01/anat/sub-01_space-orig_seg-AAL_dseg.json rename to atlas_transformed2subject_space_case2/derivatives/atlas_pipeline/sub-01/anat/sub-01_space-orig_seg-AAL_dseg.json diff --git a/atlas_within_dataset_transformed_subject_space/derivatives/atlas_pipeline/sub-01/anat/sub-01_space-orig_seg-AAL_dseg.nii.gz b/atlas_transformed2subject_space_case2/derivatives/atlas_pipeline/sub-01/anat/sub-01_space-orig_seg-AAL_dseg.nii.gz similarity index 100% rename from atlas_within_dataset_transformed_subject_space/derivatives/atlas_pipeline/sub-01/anat/sub-01_space-orig_seg-AAL_dseg.nii.gz rename to atlas_transformed2subject_space_case2/derivatives/atlas_pipeline/sub-01/anat/sub-01_space-orig_seg-AAL_dseg.nii.gz diff --git a/atlas_within_dataset_transformed_subject_space/derivatives/atlas_pipeline/sub-01/anat/sub-01_space-orig_seg-AAL_dseg.tsv b/atlas_transformed2subject_space_case2/derivatives/atlas_pipeline/sub-01/anat/sub-01_space-orig_seg-AAL_dseg.tsv similarity index 100% rename from atlas_within_dataset_transformed_subject_space/derivatives/atlas_pipeline/sub-01/anat/sub-01_space-orig_seg-AAL_dseg.tsv rename to atlas_transformed2subject_space_case2/derivatives/atlas_pipeline/sub-01/anat/sub-01_space-orig_seg-AAL_dseg.tsv diff --git a/atlas_within_dataset_transformed_subject_space/participants.json b/atlas_transformed2subject_space_case2/participants.json similarity index 100% rename from atlas_within_dataset_transformed_subject_space/participants.json rename to atlas_transformed2subject_space_case2/participants.json diff --git a/atlas_within_dataset_transformed_subject_space/participants.tsv b/atlas_transformed2subject_space_case2/participants.tsv similarity index 100% rename from atlas_within_dataset_transformed_subject_space/participants.tsv rename to atlas_transformed2subject_space_case2/participants.tsv diff --git a/atlas_within_dataset_transformed_subject_space/sub-01/anat/sub-01_T1w.json b/atlas_transformed2subject_space_case2/sub-01/anat/sub-01_T1w.json similarity index 100% rename from atlas_within_dataset_transformed_subject_space/sub-01/anat/sub-01_T1w.json rename to 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from atlas_within_dataset_transformed_template_space/atlas/atlas-HarvardOxford/atlas-HarvardOxford_space-MNI152NLin6Asym_res-1_desc-Thr25_dseg.json rename to atlas_transformed2template_space_case1/atlas/atlas-HarvardOxford/atlas-HarvardOxford_space-MNI152NLin6Asym_res-1_desc-Thr25_dseg.json diff --git a/atlas_within_dataset_transformed_template_space/atlas/atlas-HarvardOxford/atlas-HarvardOxford_space-MNI152NLin6Asym_res-1_desc-Thr25_dseg.nii.gz b/atlas_transformed2template_space_case1/atlas/atlas-HarvardOxford/atlas-HarvardOxford_space-MNI152NLin6Asym_res-1_desc-Thr25_dseg.nii.gz similarity index 100% rename from atlas_within_dataset_transformed_template_space/atlas/atlas-HarvardOxford/atlas-HarvardOxford_space-MNI152NLin6Asym_res-1_desc-Thr25_dseg.nii.gz rename to atlas_transformed2template_space_case1/atlas/atlas-HarvardOxford/atlas-HarvardOxford_space-MNI152NLin6Asym_res-1_desc-Thr25_dseg.nii.gz diff --git a/atlas_within_dataset_transformed_template_space/atlas/atlas-HarvardOxford/atlas-HarvardOxford_space-MNI152NLin6Asym_res-1_desc-Thr25_dseg.tsv b/atlas_transformed2template_space_case1/atlas/atlas-HarvardOxford/atlas-HarvardOxford_space-MNI152NLin6Asym_res-1_desc-Thr25_dseg.tsv similarity index 100% rename from atlas_within_dataset_transformed_template_space/atlas/atlas-HarvardOxford/atlas-HarvardOxford_space-MNI152NLin6Asym_res-1_desc-Thr25_dseg.tsv rename to atlas_transformed2template_space_case1/atlas/atlas-HarvardOxford/atlas-HarvardOxford_space-MNI152NLin6Asym_res-1_desc-Thr25_dseg.tsv diff --git a/atlas_within_dataset_transformed_template_space/dataset_description.json b/atlas_transformed2template_space_case1/dataset_description.json similarity index 100% rename from atlas_within_dataset_transformed_template_space/dataset_description.json rename to atlas_transformed2template_space_case1/dataset_description.json diff --git a/atlas_within_dataset_transformed_template_space/derivatives/atlas_pipeline/atlas-HarvardOxford_space-NKI_res-1_desc-Thr25_dseg.json b/atlas_transformed2template_space_case1/derivatives/atlas_pipeline/atlas-HarvardOxford_space-NKI_res-1_desc-Thr25_dseg.json similarity index 100% rename from atlas_within_dataset_transformed_template_space/derivatives/atlas_pipeline/atlas-HarvardOxford_space-NKI_res-1_desc-Thr25_dseg.json rename to atlas_transformed2template_space_case1/derivatives/atlas_pipeline/atlas-HarvardOxford_space-NKI_res-1_desc-Thr25_dseg.json diff --git a/atlas_within_dataset_transformed_template_space/derivatives/atlas_pipeline/atlas-HarvardOxford_space-NKI_res-1_desc-Thr25_dseg.nii.gz b/atlas_transformed2template_space_case1/derivatives/atlas_pipeline/atlas-HarvardOxford_space-NKI_res-1_desc-Thr25_dseg.nii.gz similarity index 100% rename from atlas_within_dataset_transformed_template_space/derivatives/atlas_pipeline/atlas-HarvardOxford_space-NKI_res-1_desc-Thr25_dseg.nii.gz rename to atlas_transformed2template_space_case1/derivatives/atlas_pipeline/atlas-HarvardOxford_space-NKI_res-1_desc-Thr25_dseg.nii.gz diff --git a/atlas_within_dataset_transformed_template_space/derivatives/atlas_pipeline/atlas-HarvardOxford_space-NKI_res-1_desc-Thr25_dseg.tsv b/atlas_transformed2template_space_case1/derivatives/atlas_pipeline/atlas-HarvardOxford_space-NKI_res-1_desc-Thr25_dseg.tsv similarity index 100% rename from atlas_within_dataset_transformed_template_space/derivatives/atlas_pipeline/atlas-HarvardOxford_space-NKI_res-1_desc-Thr25_dseg.tsv rename to atlas_transformed2template_space_case1/derivatives/atlas_pipeline/atlas-HarvardOxford_space-NKI_res-1_desc-Thr25_dseg.tsv diff --git a/atlas_within_dataset_transformed_template_space/derivatives/atlas_pipeline/dataset_description.json b/atlas_transformed2template_space_case1/derivatives/atlas_pipeline/dataset_description.json similarity index 100% rename from atlas_within_dataset_transformed_template_space/derivatives/atlas_pipeline/dataset_description.json rename to atlas_transformed2template_space_case1/derivatives/atlas_pipeline/dataset_description.json From 12e61ff2f6b6442307c6ca85fd85b558eb8fe95d Mon Sep 17 00:00:00 2001 From: CPernet Date: Fri, 26 Jan 2024 09:45:01 +0100 Subject: [PATCH 2/4] case 3 changes more likely use case --- atlas_derived_from_subjects_case3/README | 7 ++----- .../{atlas_pipeline => }/dataset_description.json | 0 .../anat/sub-01_atlas-tumour.json} | 0 .../anat/sub-01_atlas-tumour.nii.gz} | 0 .../anat/sub-01_atlas-tumour.tsv} | 0 5 files changed, 2 insertions(+), 5 deletions(-) rename atlas_derived_from_subjects_case3/derivatives/{atlas_pipeline => }/dataset_description.json (100%) rename atlas_derived_from_subjects_case3/derivatives/{atlas_pipeline/sub-01/anat/sub-01_atlas-IndividualParc_dseg.json => sub-01/anat/sub-01_atlas-tumour.json} (100%) rename atlas_derived_from_subjects_case3/derivatives/{atlas_pipeline/sub-01/anat/sub-01_atlas-IndividualParc_dseg.nii.gz => sub-01/anat/sub-01_atlas-tumour.nii.gz} (100%) rename atlas_derived_from_subjects_case3/derivatives/{atlas_pipeline/sub-01/anat/sub-01_atlas-IndividualParc_dseg.tsv => sub-01/anat/sub-01_atlas-tumour.tsv} (100%) diff --git a/atlas_derived_from_subjects_case3/README b/atlas_derived_from_subjects_case3/README index 3ac373aa7..ff9a05f0a 100644 --- a/atlas_derived_from_subjects_case3/README +++ b/atlas_derived_from_subjects_case3/README @@ -1,12 +1,9 @@ -This example dataset aims to showcase the different use cases supported by `BIDS Atlas`, ie [BEP038](https://docs.google.com/document/d/1RxW4cARr3-EiBEcXjLpSIVidvnUSHE7yJCUY91i5TfM/edit?usp=sharing) and thus also evaluating and testing the proposed changes to the specification. - -Only the imaging files, ie `*.nii.gz` have been truncated to `0 bytes`, while all other files, ie the `.tsv` `LookUpTables` and `JSON` metadata are provided in full. +This example dataset aims to showcase subject specific atlases. Only the imaging files, ie `*.nii.gz` have been truncated to `0 bytes`, while all other files, ie the `.tsv` `LookUpTables` and `JSON` metadata are provided in full. # BIDS Atlas use cases and respective atlases -In order to cover the use cases of this `BEP`, the dataset at hand entails multiple `atlases` as indicated below. `Atlases` are utilized in `BIDS-Atlas` in **two general ways**: as `DataSet` of type `atlas` in case an atlas (or multiple) is provided solely and as-is and within a `DataSet` of type `raw` or `derivative`. In the latter case, `non-altered`/`original` `atlases` are stored at `BIDS root` and `altered`/`derived`/`applied` `atlases` are stored under `derivatives`. ## Atlas-within-dataset - atlas derived within a given subject -The example provided here refers to "atlas-within-dataset" use case, specifically use cases where an `atlas` is derived within a given `subject` only. \ No newline at end of file +The example provided here refers to "atlas-within-dataset" use case, specifically use cases where an `atlas` is derived within a given `subject` only. It is illustrated here with the `atlas` being a set a maps describing tumour specific locations. Other atlases could be set of histological maps (in such case the _coordsystem.json would be needded to match image coordinates and reference frames). \ No newline at end of file diff --git a/atlas_derived_from_subjects_case3/derivatives/atlas_pipeline/dataset_description.json b/atlas_derived_from_subjects_case3/derivatives/dataset_description.json similarity index 100% rename from atlas_derived_from_subjects_case3/derivatives/atlas_pipeline/dataset_description.json rename to atlas_derived_from_subjects_case3/derivatives/dataset_description.json diff --git a/atlas_derived_from_subjects_case3/derivatives/atlas_pipeline/sub-01/anat/sub-01_atlas-IndividualParc_dseg.json b/atlas_derived_from_subjects_case3/derivatives/sub-01/anat/sub-01_atlas-tumour.json similarity index 100% rename from atlas_derived_from_subjects_case3/derivatives/atlas_pipeline/sub-01/anat/sub-01_atlas-IndividualParc_dseg.json rename to atlas_derived_from_subjects_case3/derivatives/sub-01/anat/sub-01_atlas-tumour.json diff --git a/atlas_derived_from_subjects_case3/derivatives/atlas_pipeline/sub-01/anat/sub-01_atlas-IndividualParc_dseg.nii.gz b/atlas_derived_from_subjects_case3/derivatives/sub-01/anat/sub-01_atlas-tumour.nii.gz similarity index 100% rename from atlas_derived_from_subjects_case3/derivatives/atlas_pipeline/sub-01/anat/sub-01_atlas-IndividualParc_dseg.nii.gz rename to atlas_derived_from_subjects_case3/derivatives/sub-01/anat/sub-01_atlas-tumour.nii.gz diff --git a/atlas_derived_from_subjects_case3/derivatives/atlas_pipeline/sub-01/anat/sub-01_atlas-IndividualParc_dseg.tsv b/atlas_derived_from_subjects_case3/derivatives/sub-01/anat/sub-01_atlas-tumour.tsv similarity index 100% rename from atlas_derived_from_subjects_case3/derivatives/atlas_pipeline/sub-01/anat/sub-01_atlas-IndividualParc_dseg.tsv rename to atlas_derived_from_subjects_case3/derivatives/sub-01/anat/sub-01_atlas-tumour.tsv From bad9a966137920adbeecfac23ad27886a6908bd4 Mon Sep 17 00:00:00 2001 From: CPernet Date: Fri, 26 Jan 2024 09:50:22 +0100 Subject: [PATCH 3/4] oh that is not a derivative --- .../derivatives/dataset_description.json | 6 ------ .../{derivatives => }/sub-01/anat/sub-01_atlas-tumour.json | 0 .../sub-01/anat/sub-01_atlas-tumour.nii.gz | 0 .../{derivatives => }/sub-01/anat/sub-01_atlas-tumour.tsv | 0 4 files changed, 6 deletions(-) delete mode 100644 atlas_derived_from_subjects_case3/derivatives/dataset_description.json rename atlas_derived_from_subjects_case3/{derivatives => }/sub-01/anat/sub-01_atlas-tumour.json (100%) rename atlas_derived_from_subjects_case3/{derivatives => }/sub-01/anat/sub-01_atlas-tumour.nii.gz (100%) rename atlas_derived_from_subjects_case3/{derivatives => }/sub-01/anat/sub-01_atlas-tumour.tsv (100%) diff --git a/atlas_derived_from_subjects_case3/derivatives/dataset_description.json b/atlas_derived_from_subjects_case3/derivatives/dataset_description.json deleted file mode 100644 index dec9bedf3..000000000 --- a/atlas_derived_from_subjects_case3/derivatives/dataset_description.json +++ /dev/null @@ -1,6 +0,0 @@ -{ - "BIDSVersion": "1.0.0", - "License": "CC0", - "Name": "BIDS Atlas within dataset example - atlas derived within a given subject only", - "DatasetType": "derivative" -} \ No newline at end of file diff --git a/atlas_derived_from_subjects_case3/derivatives/sub-01/anat/sub-01_atlas-tumour.json b/atlas_derived_from_subjects_case3/sub-01/anat/sub-01_atlas-tumour.json similarity index 100% rename from atlas_derived_from_subjects_case3/derivatives/sub-01/anat/sub-01_atlas-tumour.json rename to atlas_derived_from_subjects_case3/sub-01/anat/sub-01_atlas-tumour.json diff --git a/atlas_derived_from_subjects_case3/derivatives/sub-01/anat/sub-01_atlas-tumour.nii.gz b/atlas_derived_from_subjects_case3/sub-01/anat/sub-01_atlas-tumour.nii.gz similarity index 100% rename from atlas_derived_from_subjects_case3/derivatives/sub-01/anat/sub-01_atlas-tumour.nii.gz rename to atlas_derived_from_subjects_case3/sub-01/anat/sub-01_atlas-tumour.nii.gz diff --git a/atlas_derived_from_subjects_case3/derivatives/sub-01/anat/sub-01_atlas-tumour.tsv b/atlas_derived_from_subjects_case3/sub-01/anat/sub-01_atlas-tumour.tsv similarity index 100% rename from atlas_derived_from_subjects_case3/derivatives/sub-01/anat/sub-01_atlas-tumour.tsv rename to atlas_derived_from_subjects_case3/sub-01/anat/sub-01_atlas-tumour.tsv From c5a12d7f84ca1cd976e4b8e14706afdadbf30e34 Mon Sep 17 00:00:00 2001 From: CPernet Date: Fri, 26 Jan 2024 09:55:25 +0100 Subject: [PATCH 4/4] use inheritence --- .../{sub-01/anat/sub-01_atlas-tumour.tsv => atlas-tumour.tsv} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename atlas_derived_from_subjects_case3/{sub-01/anat/sub-01_atlas-tumour.tsv => atlas-tumour.tsv} (100%) diff --git a/atlas_derived_from_subjects_case3/sub-01/anat/sub-01_atlas-tumour.tsv b/atlas_derived_from_subjects_case3/atlas-tumour.tsv similarity index 100% rename from atlas_derived_from_subjects_case3/sub-01/anat/sub-01_atlas-tumour.tsv rename to atlas_derived_from_subjects_case3/atlas-tumour.tsv