PESTILLILAB · CPernet · Jan 26, 2024 · Jan 26, 2024 · Jan 26, 2024 · Jan 26, 2024
diff --git a/...thin_dataset_derived_subject_space/README → atlas_derived_from_subjects_case3/README b/...thin_dataset_derived_subject_space/README → 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.
+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).  
diff --git a/...anat/sub-01_atlas-IndividualParc_dseg.tsv → ...ived_from_subjects_case3/atlas-tumour.tsv b/...anat/sub-01_atlas-IndividualParc_dseg.tsv → ...ived_from_subjects_case3/atlas-tumour.tsv
diff --git a/...ed_subject_space/dataset_description.json → ...m_subjects_case3/dataset_description.json b/...ed_subject_space/dataset_description.json → ...m_subjects_case3/dataset_description.json
diff --git a/...t_derived_subject_space/participants.json → ...ved_from_subjects_case3/participants.json b/...t_derived_subject_space/participants.json → ...ved_from_subjects_case3/participants.json
diff --git a/...et_derived_subject_space/participants.tsv → ...ived_from_subjects_case3/participants.tsv b/...et_derived_subject_space/participants.tsv → ...ived_from_subjects_case3/participants.tsv
diff --git a/...subject_space/sub-01/anat/sub-01_T1w.json → ...ubjects_case3/sub-01/anat/sub-01_T1w.json b/...subject_space/sub-01/anat/sub-01_T1w.json → ...ubjects_case3/sub-01/anat/sub-01_T1w.json
diff --git a/...bject_space/sub-01/anat/sub-01_T1w.nii.gz → ...jects_case3/sub-01/anat/sub-01_T1w.nii.gz b/...bject_space/sub-01/anat/sub-01_T1w.nii.gz → ...jects_case3/sub-01/anat/sub-01_T1w.nii.gz
diff --git a/...nat/sub-01_atlas-IndividualParc_dseg.json → ...ase3/sub-01/anat/sub-01_atlas-tumour.json b/...nat/sub-01_atlas-IndividualParc_dseg.json → ...ase3/sub-01/anat/sub-01_atlas-tumour.json
diff --git a/...t/sub-01_atlas-IndividualParc_dseg.nii.gz → ...e3/sub-01/anat/sub-01_atlas-tumour.nii.gz b/...t/sub-01_atlas-IndividualParc_dseg.nii.gz → ...e3/sub-01/anat/sub-01_atlas-tumour.nii.gz
diff --git a/..._dataset_transformed_subject_space/README → atlas_transformed2subject_space_case2/README b/..._dataset_transformed_subject_space/README → atlas_transformed2subject_space_case2/README
diff --git a/...AAL_space-MNI152NLin6Asym_res-1_dseg.json → ...AAL_space-MNI152NLin6Asym_res-1_dseg.json b/...AAL_space-MNI152NLin6Asym_res-1_dseg.json → ...AAL_space-MNI152NLin6Asym_res-1_dseg.json
diff --git a/...L_space-MNI152NLin6Asym_res-1_dseg.nii.gz → ...L_space-MNI152NLin6Asym_res-1_dseg.nii.gz b/...L_space-MNI152NLin6Asym_res-1_dseg.nii.gz → ...L_space-MNI152NLin6Asym_res-1_dseg.nii.gz
diff --git a/...-AAL_space-MNI152NLin6Asym_res-1_dseg.tsv → ...-AAL_space-MNI152NLin6Asym_res-1_dseg.tsv b/...-AAL_space-MNI152NLin6Asym_res-1_dseg.tsv → ...-AAL_space-MNI152NLin6Asym_res-1_dseg.tsv
diff --git a/...ed_subject_space/dataset_description.json → ...ject_space_case2/dataset_description.json b/...ed_subject_space/dataset_description.json → ...ject_space_case2/dataset_description.json
diff --git a/...s/atlas_pipeline/dataset_description.json → ...s/atlas_pipeline/dataset_description.json b/...s/atlas_pipeline/dataset_description.json → ...s/atlas_pipeline/dataset_description.json
diff --git a/.../anat/sub-01_space-orig_seg-AAL_dseg.json → .../anat/sub-01_space-orig_seg-AAL_dseg.json b/.../anat/sub-01_space-orig_seg-AAL_dseg.json → .../anat/sub-01_space-orig_seg-AAL_dseg.json
diff --git a/...nat/sub-01_space-orig_seg-AAL_dseg.nii.gz → ...nat/sub-01_space-orig_seg-AAL_dseg.nii.gz b/...nat/sub-01_space-orig_seg-AAL_dseg.nii.gz → ...nat/sub-01_space-orig_seg-AAL_dseg.nii.gz
diff --git a/...1/anat/sub-01_space-orig_seg-AAL_dseg.tsv → ...1/anat/sub-01_space-orig_seg-AAL_dseg.tsv b/...1/anat/sub-01_space-orig_seg-AAL_dseg.tsv → ...1/anat/sub-01_space-orig_seg-AAL_dseg.tsv
diff --git a/...ansformed_subject_space/participants.json → ...med2subject_space_case2/participants.json b/...ansformed_subject_space/participants.json → ...med2subject_space_case2/participants.json
diff --git a/...ransformed_subject_space/participants.tsv → ...rmed2subject_space_case2/participants.tsv b/...ransformed_subject_space/participants.tsv → ...rmed2subject_space_case2/participants.tsv
diff --git a/...subject_space/sub-01/anat/sub-01_T1w.json → ...t_space_case2/sub-01/anat/sub-01_T1w.json b/...subject_space/sub-01/anat/sub-01_T1w.json → ...t_space_case2/sub-01/anat/sub-01_T1w.json
diff --git a/...bject_space/sub-01/anat/sub-01_T1w.nii.gz → ...space_case2/sub-01/anat/sub-01_T1w.nii.gz b/...bject_space/sub-01/anat/sub-01_T1w.nii.gz → ...space_case2/sub-01/anat/sub-01_T1w.nii.gz
diff --git a/...dataset_transformed_template_space/README → ...s_transformed2template_space_case1/README b/...dataset_transformed_template_space/README → ...s_transformed2template_space_case1/README
diff --git a/...NI152NLin6Asym_res-1_desc-Thr25_dseg.json → ...NI152NLin6Asym_res-1_desc-Thr25_dseg.json b/...NI152NLin6Asym_res-1_desc-Thr25_dseg.json → ...NI152NLin6Asym_res-1_desc-Thr25_dseg.json
diff --git a/...152NLin6Asym_res-1_desc-Thr25_dseg.nii.gz → ...152NLin6Asym_res-1_desc-Thr25_dseg.nii.gz b/...152NLin6Asym_res-1_desc-Thr25_dseg.nii.gz → ...152NLin6Asym_res-1_desc-Thr25_dseg.nii.gz
diff --git a/...MNI152NLin6Asym_res-1_desc-Thr25_dseg.tsv → ...MNI152NLin6Asym_res-1_desc-Thr25_dseg.tsv b/...MNI152NLin6Asym_res-1_desc-Thr25_dseg.tsv → ...MNI152NLin6Asym_res-1_desc-Thr25_dseg.tsv
diff --git a/...d_template_space/dataset_description.json → ...late_space_case1/dataset_description.json b/...d_template_space/dataset_description.json → ...late_space_case1/dataset_description.json
diff --git a/...ford_space-NKI_res-1_desc-Thr25_dseg.json → ...ford_space-NKI_res-1_desc-Thr25_dseg.json b/...ford_space-NKI_res-1_desc-Thr25_dseg.json → ...ford_space-NKI_res-1_desc-Thr25_dseg.json
diff --git a/...rd_space-NKI_res-1_desc-Thr25_dseg.nii.gz → ...rd_space-NKI_res-1_desc-Thr25_dseg.nii.gz b/...rd_space-NKI_res-1_desc-Thr25_dseg.nii.gz → ...rd_space-NKI_res-1_desc-Thr25_dseg.nii.gz
diff --git a/...xford_space-NKI_res-1_desc-Thr25_dseg.tsv → ...xford_space-NKI_res-1_desc-Thr25_dseg.tsv b/...xford_space-NKI_res-1_desc-Thr25_dseg.tsv → ...xford_space-NKI_res-1_desc-Thr25_dseg.tsv
diff --git a/...s/atlas_pipeline/dataset_description.json → ...s/atlas_pipeline/dataset_description.json b/...s/atlas_pipeline/dataset_description.json → ...s/atlas_pipeline/dataset_description.json
diff --git a/..._within_dataset_derived_subject_space/derivatives/atlas_pipeline/dataset_description.json b/..._within_dataset_derived_subject_space/derivatives/atlas_pipeline/dataset_description.json