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FIX: update PET examples
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@mnoergaard
mnoergaard committed Oct 23, 2024
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Showing 1 changed file with 76 additions and 84 deletions.
160 changes: 76 additions & 84 deletions src/derivatives/atlas.md
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Expand Up @@ -276,7 +276,7 @@ A guide for using macros can be found at
})
}}

**Defining atlases referenced to a pre-existing template.**
**Defining atlases and templates referenced to a pre-existing template.**
Once a standard space is instantiated by a reference template,
atlasing knowledge MAY be specified employing the
[`atlas-<label>` entity](../glossary.md#atlas-entities).
Expand Down Expand Up @@ -355,8 +355,8 @@ A guide for using macros can be found at
})
}}

For example, the [PS13 atlas](https://doi.org/10.18112/openneuro.ds004401.v1.3.0),
a molecular imaging brain atlas of Cyclooxygenase-1 (PET),
For example, the [PS13 template](https://doi.org/10.18112/openneuro.ds004401.v1.3.0),
a molecular imaging brain template of Cyclooxygenase-1 (PET),
was generated in two standard spaces: `MNI152Lin` and `fsaverage`:

<!-- This block generates a file tree.
Expand All @@ -365,70 +365,66 @@ A guide for using macros can be found at
-->
{{ MACROS___make_filetree_example({
"ps13-pipeline": {
"tpl-fsaverage": {
"tpl-ps13": {
"pet": {
"tpl-fsaverage_atlas-ps13_desc-nopvc_dseg.nii.gz": "",
"tpl-fsaverage_atlas-ps13_desc-pvc_dseg.nii.gz": "",
"tpl-fsaverage_atlas-ps13_dseg.json": "",
"tpl-fsaverage_atlas-ps13_dseg.tsv": "",
"tpl-fsaverage_desc-nopvc_pet.json": "",
"tpl-fsaverage_desc-nopvc_pet.nii.gz": "",
"tpl-fsaverage_desc-pvc_pet.json": "",
"tpl-fsaverage_desc-pvc_pet.nii.gz": "",
"tpl-fsaverage_hemi-L_den-164k_desc-nopvc_pet.json": "",
"tpl-fsaverage_hemi-L_den-164k_desc-nopvc_pet.shape.gii": "",
"tpl-fsaverage_hemi-L_den-164k_desc-pvc_pet.json": "",
"tpl-fsaverage_hemi-L_den-164k_desc-pvc_pet.shape.gii": "",
"tpl-fsaverage_hemi-L_den-164k_stat-std_desc-nopvc_pet.json": "",
"tpl-fsaverage_hemi-L_den-164k_stat-std_desc-nopvc_pet.shape.gii": "",
"tpl-fsaverage_hemi-L_den-164k_stat-std_desc-pvc_pet.json": "",
"tpl-fsaverage_hemi-L_den-164k_stat-std_desc-pvc_pet.shape.gii": "",
"tpl-fsaverage_hemi-R_den-164k_desc-nopvc_pet.json": "",
"tpl-fsaverage_hemi-R_den-164k_desc-nopvc_pet.shape.gii": "",
"tpl-fsaverage_hemi-R_den-164k_desc-pvc_pet.json": "",
"tpl-fsaverage_hemi-R_den-164k_desc-pvc_pet.shape.gii": "",
"tpl-fsaverage_hemi-R_den-164k_stat-std_desc-nopvc_pet.json": "",
"tpl-fsaverage_hemi-R_den-164k_stat-std_desc-nopvc_pet.shape.gii": "",
"tpl-fsaverage_hemi-R_den-164k_stat-std_desc-pvc_pet.json": "",
"tpl-fsaverage_hemi-R_den-164k_stat-std_desc-pvc_pet.shape.gii": "",
"tpl-fsaverage_stat-std_desc-nopvc_pet.json": "",
"tpl-fsaverage_stat-std_desc-nopvc_pet.nii.gz": "",
"tpl-fsaverage_stat-std_desc-pvc_pet.json": "",
"tpl-fsaverage_stat-std_desc-pvc_pet.nii.gz": "",
"tpl-ps13_space-fsaverage_atlas-ps13_desc-nopvc_dseg.nii.gz": "",
"tpl-ps13_space-fsaverage_atlas-ps13_desc-pvc_dseg.nii.gz": "",
"tpl-ps13_space-fsaverage_atlas-ps13_dseg.json": "",
"tpl-ps13_space-fsaverage_atlas-ps13_dseg.tsv": "",
"tpl-ps13_space-fsaverage_desc-nopvc_pet.json": "",
"tpl-ps13_space-fsaverage_desc-nopvc_pet.nii.gz": "",
"tpl-ps13_space-fsaverage_desc-pvc_pet.json": "",
"tpl-ps13_space-fsaverage_desc-pvc_pet.nii.gz": "",
"tpl-ps13_space-fsaverage_hemi-L_den-164k_desc-nopvc_pet.json": "",
"tpl-ps13_space-fsaverage_hemi-L_den-164k_desc-nopvc_pet.shape.gii": "",
"tpl-ps13_space-fsaverage-L_den-164k_desc-pvc_pet.json": "",
"tpl-ps13_space-fsaverage-L_den-164k_desc-pvc_pet.shape.gii": "",
"tpl-ps13_space-fsaverage_hemi-L_den-164k_stat-std_desc-nopvc_pet.json": "",
"tpl-ps13_space-fsaverage_hemi-L_den-164k_stat-std_desc-nopvc_pet.shape.gii": "",
"tpl-ps13_space-fsaverage_hemi-L_den-164k_stat-std_desc-pvc_pet.json": "",
"tpl-ps13_space-fsaverage_hemi-L_den-164k_stat-std_desc-pvc_pet.shape.gii": "",
"tpl-ps13_space-fsaverage_hemi-R_den-164k_desc-nopvc_pet.json": "",
"tpl-ps13_space-fsaverage_hemi-R_den-164k_desc-nopvc_pet.shape.gii": "",
"tpl-ps13_space-fsaverage_hemi-R_den-164k_desc-pvc_pet.json": "",
"tpl-ps13_space-fsaverage_hemi-R_den-164k_desc-pvc_pet.shape.gii": "",
"tpl-ps13_space-fsaverage_hemi-R_den-164k_stat-std_desc-nopvc_pet.json": "",
"tpl-ps13_space-fsaverage_hemi-R_den-164k_stat-std_desc-nopvc_pet.shape.gii": "",
"tpl-ps13_space-fsaverage_hemi-R_den-164k_stat-std_desc-pvc_pet.json": "",
"tpl-ps13_space-fsaverage_hemi-R_den-164k_stat-std_desc-pvc_pet.shape.gii": "",
"tpl-ps13_space-fsaverage_stat-std_desc-nopvc_pet.json": "",
"tpl-ps13_space-fsaverage_stat-std_desc-nopvc_pet.nii.gz": "",
"tpl-ps13_space-fsaverage_stat-std_desc-pvc_pet.json": "",
"tpl-ps13_space-fsaverage_stat-std_desc-pvc_pet.nii.gz": "",
"tpl-ps13_space-MNI152Lin_atlas-ps13_desc-nopvc_dseg.nii.gz": "",
"tpl-ps13_space-MNI152Lin_atlas-ps13_desc-pvc_dseg.nii.gz": "",
"tpl-ps13_space-MNI152Lin_atlas-ps13_dseg.json": "",
"tpl-ps13_space-MNI152Lin_atlas-ps13_dseg.tsv": "",
"tpl-ps13_space-MNI152Lin_res-1p5_desc-spmvbmNopvc_pet.json": "",
"tpl-ps13_space-MNI152Lin_res-1p5_desc-spmvbmNopvc_pet.nii.gz": "",
"tpl-ps13_space-MNI152Lin_res-1p5_desc-spmvbmPvc_pet.json": "",
"tpl-ps13_space-MNI152Lin_res-1p5_desc-spmvbmPvc_pet.nii.gz": "",
"tpl-ps13_space-MNI152Lin_res-1p5_stat-std_desc-spmvbmNopvc_pet.json": "",
"tpl-ps13_space-MNI152Lin_res-1p5_stat-std_desc-spmvbmNopvc_pet.nii.gz": "",
"tpl-ps13_space-MNI152Lin_res-1p5_stat-std_desc-spmvbmPvc_pet.json": "",
"tpl-ps13_space-MNI152Lin_res-1p5_stat-std_desc-spmvbmPvc_pet.nii.gz": "",
"tpl-ps13_space-MNI152Lin_res-2_desc-fnirtNopvc_pet.json": "",
"tpl-ps13_space-MNI152Lin_res-2_desc-fnirtNopvc_pet.nii.gz": "",
"tpl-ps13_space-MNI152Lin_res-2_desc-fnirtPvc_pet.json": "",
"tpl-ps13_space-MNI152Lin_res-2_desc-fnirtPvc_pet.nii.gz": "",
"tpl-ps13_space-MNI152Lin_res-2_desc-nopvc_pet.json": "",
"tpl-ps13_space-MNI152Lin_res-2_desc-nopvc_pet.nii.gz": "",
"tpl-ps13_space-MNI152Lin_res-2_desc-pvc_pet.json": "",
"tpl-ps13_space-MNI152Lin_res-2_desc-pvc_pet.nii.gz": "",
"tpl-ps13_space-MNI152Lin_res-2_stat-std_desc-fnirtNopvc_pet.json": "",
"tpl-ps13_space-MNI152Lin_res-2_stat-std_desc-fnirtNopvc_pet.nii.gz": "",
"tpl-ps13_space-MNI152Lin_res-2_stat-std_desc-fnirtPvc_pet.json": "",
"tpl-ps13_space-MNI152Lin_res-2_stat-std_desc-fnirtPvc_pet.nii.gz": "",
"tpl-ps13_space-MNI152Lin_res-2_stat-std_desc-nopvc_pet.json": "",
"tpl-ps13_space-MNI152Lin_res-2_stat-std_desc-nopvc_pet.nii.gz": "",
"tpl-ps13_space-MNI152Lin_res-2_stat-std_desc-pvc_pet.json": "",
"tpl-ps13_space-MNI152Lin_res-2_stat-std_desc-pvc_pet.nii.gz": "",
},
},
"tpl-MNI152Lin": {
"pet": {
"tpl-MNI152Lin_atlas-ps13_desc-nopvc_dseg.nii.gz": "",
"tpl-MNI152Lin_atlas-ps13_desc-pvc_dseg.nii.gz": "",
"tpl-MNI152Lin_atlas-ps13_dseg.json": "",
"tpl-MNI152Lin_atlas-ps13_dseg.tsv": "",
"tpl-MNI152Lin_res-1p5_desc-spmvbmNopvc_pet.json": "",
"tpl-MNI152Lin_res-1p5_desc-spmvbmNopvc_pet.nii.gz": "",
"tpl-MNI152Lin_res-1p5_desc-spmvbmPvc_pet.json": "",
"tpl-MNI152Lin_res-1p5_desc-spmvbmPvc_pet.nii.gz": "",
"tpl-MNI152Lin_res-1p5_stat-std_desc-spmvbmNopvc_pet.json": "",
"tpl-MNI152Lin_res-1p5_stat-std_desc-spmvbmNopvc_pet.nii.gz": "",
"tpl-MNI152Lin_res-1p5_stat-std_desc-spmvbmPvc_pet.json": "",
"tpl-MNI152Lin_res-1p5_stat-std_desc-spmvbmPvc_pet.nii.gz": "",
"tpl-MNI152Lin_res-2_desc-fnirtNopvc_pet.json": "",
"tpl-MNI152Lin_res-2_desc-fnirtNopvc_pet.nii.gz": "",
"tpl-MNI152Lin_res-2_desc-fnirtPvc_pet.json": "",
"tpl-MNI152Lin_res-2_desc-fnirtPvc_pet.nii.gz": "",
"tpl-MNI152Lin_res-2_desc-nopvc_pet.json": "",
"tpl-MNI152Lin_res-2_desc-nopvc_pet.nii.gz": "",
"tpl-MNI152Lin_res-2_desc-pvc_pet.json": "",
"tpl-MNI152Lin_res-2_desc-pvc_pet.nii.gz": "",
"tpl-MNI152Lin_res-2_stat-std_desc-fnirtNopvc_pet.json": "",
"tpl-MNI152Lin_res-2_stat-std_desc-fnirtNopvc_pet.nii.gz": "",
"tpl-MNI152Lin_res-2_stat-std_desc-fnirtPvc_pet.json": "",
"tpl-MNI152Lin_res-2_stat-std_desc-fnirtPvc_pet.nii.gz": "",
"tpl-MNI152Lin_res-2_stat-std_desc-nopvc_pet.json": "",
"tpl-MNI152Lin_res-2_stat-std_desc-nopvc_pet.nii.gz": "",
"tpl-MNI152Lin_res-2_stat-std_desc-pvc_pet.json": "",
"tpl-MNI152Lin_res-2_stat-std_desc-pvc_pet.nii.gz": "",
},
}
}
})
}}
Expand All @@ -449,28 +445,24 @@ A guide for using macros can be found at
"ps13rev2034-pipeline": {
"tpl-fsaverage": {
"pet": {
"tpl-fsaverage_atlas-ps13_desc-nopvc_dseg.nii.gz": "",
"tpl-fsaverage_atlas-ps13_desc-pvc_dseg.nii.gz": "",
"tpl-fsaverage_atlas-ps13_dseg.json": "",
"tpl-fsaverage_atlas-ps13_dseg.tsv": "",
"tpl-fsaverage_atlas-ps13_hemi-L_den-164k_desc-nopvc_pet.json": "",
"tpl-ps13_space-fsaverage_atlas-ps13_desc-nopvc_dseg.nii.gz": "",
"tpl-ps13_space-fsaverage_atlas-ps13_desc-pvc_dseg.nii.gz": "",
"tpl-ps13_space-fsaverage_atlas-ps13_dseg.json": "",
"tpl-ps13_space-fsaverage_atlas-ps13_dseg.tsv": "",
"tpl-ps13_space-fsaverage_atlas-ps13_hemi-L_den-164k_desc-nopvc_pet.json": "",
"tpl-ps13_space-fsaverage_atlas-ps13_stat-std_desc-pvc_pet.nii.gz": "",
"...": "",
"tpl-fsaverage_atlas-ps13_stat-std_desc-pvc_pet.nii.gz": "",
},
},
"tpl-MNI152Lin": {
"pet": {
"tpl-MNI152Lin_atlas-ps13_desc-nopvc_dseg.nii.gz": "",
"tpl-MNI152Lin_atlas-ps13_desc-pvc_dseg.nii.gz": "",
"tpl-MNI152Lin_atlas-ps13_dseg.json": "",
"tpl-MNI152Lin_atlas-ps13_dseg.tsv": "",
"tpl-MNI152Lin_atlas-ps13_res-1p5_desc-spmvbmNopvc_pet.json": "",
"tpl-ps13_space-MNI152Lin_atlas-ps13_desc-nopvc_dseg.nii.gz": "",
"tpl-ps13_space-MNI152Lin_atlas-ps13_desc-pvc_dseg.nii.gz": "",
"tpl-ps13_space-MNI152Lin_atlas-ps13_dseg.json": "",
"tpl-ps13_space-MNI152Lin_atlas-ps13_dseg.tsv": "",
"tpl-ps13_space-MNI152Lin_atlas-ps13_res-1p5_desc-spmvbmNopvc_pet.json": "",
"tpl-ps13_space-MNI152Lin_atlas-ps13_res-2_stat-std_desc-pvc_pet.nii.gz": "",
"tpl-ps13_space-MNI152Lin_atlas-ps13rev2034_desc-nopvc_dseg.nii.gz": "",
"tpl-ps13_space-MNI152Lin_atlas-ps13rev2034_desc-pvc_dseg.nii.gz": "",
"tpl-ps13_space-MNI152Lin_atlas-ps13rev2034_dseg.json": "",
"tpl-ps13_space-MNI152Lin_atlas-ps13rev2034_dseg.tsv": "",
"...": "",
"tpl-MNI152Lin_atlas-ps13_res-2_stat-std_desc-pvc_pet.nii.gz": "",
"tpl-MNI152Lin_atlas-ps13rev2034_desc-nopvc_dseg.nii.gz": "",
"tpl-MNI152Lin_atlas-ps13rev2034_desc-pvc_dseg.nii.gz": "",
"tpl-MNI152Lin_atlas-ps13rev2034_dseg.json": "",
"tpl-MNI152Lin_atlas-ps13rev2034_dseg.tsv": "",
},
}
}
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