From 66bbba11b9cc0ac5fdf9389bf5aaad1670e9d950 Mon Sep 17 00:00:00 2001 From: Arman Jahanpour <77515879+rmanaem@users.noreply.github.com> Date: Wed, 20 Nov 2024 13:33:40 -0500 Subject: [PATCH] [MNT] Updated `query-tool-results` files (#44) * Updated files * Updated `query-tool-results` files --- .../cohort-participant-machine-results.tsv | 21 +++++++++++++ .../cohort-participant-results-agg.tsv | 2 ++ .../cohort-participant-results.tsv | 21 +++++++++++++ query-tool-results/dataset-level-results.tsv | 2 -- .../participant-level-results-agg.tsv | 2 -- .../participant-level-results.tsv | 31 ------------------- 6 files changed, 44 insertions(+), 35 deletions(-) create mode 100644 query-tool-results/cohort-participant-machine-results.tsv create mode 100644 query-tool-results/cohort-participant-results-agg.tsv create mode 100644 query-tool-results/cohort-participant-results.tsv delete mode 100644 query-tool-results/dataset-level-results.tsv delete mode 100644 query-tool-results/participant-level-results-agg.tsv delete mode 100644 query-tool-results/participant-level-results.tsv diff --git a/query-tool-results/cohort-participant-machine-results.tsv b/query-tool-results/cohort-participant-machine-results.tsv new file mode 100644 index 0000000..9b68a0b --- /dev/null +++ b/query-tool-results/cohort-participant-machine-results.tsv @@ -0,0 +1,21 @@ +DatasetName PortalURI SubjectID SessionID SessionFilePath SessionType NumMatchingPhenotypicSessions NumMatchingImagingSessions SessionImagingModalities SessionCompletedPipelines DatasetImagingModalities DatasetPipelines +BIDS synthetic https://github.com/bids-standard/bids-examples sub-01 ses-01 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-01/ses-01 http://neurobagel.org/vocab/ImagingSession 2 2 http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples sub-01 ses-01 http://neurobagel.org/vocab/PhenotypicSession 2 2 http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples sub-01 ses-02 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-01/ses-02 http://neurobagel.org/vocab/ImagingSession 2 2 http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples sub-01 ses-02 http://neurobagel.org/vocab/PhenotypicSession 2 2 http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples sub-02 ses-01 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-02/ses-01 http://neurobagel.org/vocab/ImagingSession 2 2 http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples sub-02 ses-01 http://neurobagel.org/vocab/PhenotypicSession 2 2 http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples sub-02 ses-02 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-02/ses-02 http://neurobagel.org/vocab/ImagingSession 2 2 http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples sub-02 ses-02 http://neurobagel.org/vocab/PhenotypicSession 2 2 http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples sub-03 ses-01 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-03/ses-01 http://neurobagel.org/vocab/ImagingSession 2 2 http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples sub-03 ses-01 http://neurobagel.org/vocab/PhenotypicSession 2 2 http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples sub-03 ses-02 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-03/ses-02 http://neurobagel.org/vocab/ImagingSession 2 2 http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples sub-03 ses-02 http://neurobagel.org/vocab/PhenotypicSession 2 2 http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples sub-04 ses-01 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-04/ses-01 http://neurobagel.org/vocab/ImagingSession 2 2 http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples sub-04 ses-01 http://neurobagel.org/vocab/PhenotypicSession 2 2 http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples sub-04 ses-02 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-04/ses-02 http://neurobagel.org/vocab/ImagingSession 2 2 http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples sub-04 ses-02 http://neurobagel.org/vocab/PhenotypicSession 2 2 http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples sub-05 ses-01 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-05/ses-01 http://neurobagel.org/vocab/ImagingSession 2 2 http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples sub-05 ses-01 http://neurobagel.org/vocab/PhenotypicSession 2 2 http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples sub-05 ses-02 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-05/ses-02 http://neurobagel.org/vocab/ImagingSession 2 2 http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples sub-05 ses-02 http://neurobagel.org/vocab/PhenotypicSession 2 2 http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 \ No newline at end of file diff --git a/query-tool-results/cohort-participant-results-agg.tsv b/query-tool-results/cohort-participant-results-agg.tsv new file mode 100644 index 0000000..445bc89 --- /dev/null +++ b/query-tool-results/cohort-participant-results-agg.tsv @@ -0,0 +1,2 @@ +DatasetName PortalURI NumMatchingSubjects SubjectID SessionID SessionFilePath SessionType Age Sex Diagnosis Assessment NumMatchingPhenotypicSessions NumMatchingImagingSessions SessionImagingModalities SessionCompletedPipelines DatasetImagingModalities DatasetPipelines +BIDS synthetic https://github.com/bids-standard/bids-examples 5 protected protected protected protected protected protected protected protected protected protected protected protected Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 \ No newline at end of file diff --git a/query-tool-results/cohort-participant-results.tsv b/query-tool-results/cohort-participant-results.tsv new file mode 100644 index 0000000..57e472c --- /dev/null +++ b/query-tool-results/cohort-participant-results.tsv @@ -0,0 +1,21 @@ +DatasetName PortalURI NumMatchingSubjects SubjectID SessionID SessionFilePath SessionType Age Sex Diagnosis Assessment NumMatchingPhenotypicSessions NumMatchingImagingSessions SessionImagingModalities SessionCompletedPipelines DatasetImagingModalities DatasetPipelines +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-01 ses-01 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-01/ses-01 Imaging 2 2 T1 Weighted, Flow Weighted fmriprep 23.1.3, freesurfer 7.3.2 Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-01 ses-01 Phenotypic 34.1 female Montreal Cognitive Assessment, Unified Parkinson's Disease Rating Scale 2 2 Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-01 ses-02 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-01/ses-02 Imaging 2 2 T1 Weighted, Flow Weighted Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-01 ses-02 Phenotypic 35.3 female Montreal Cognitive Assessment, Unified Parkinson's Disease Rating Scale 2 2 Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-02 ses-01 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-02/ses-01 Imaging 2 2 T1 Weighted, Flow Weighted fmriprep 23.1.3, freesurfer 7.3.2 Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-02 ses-01 Phenotypic male Attention deficit hyperactivity disorder Montreal Cognitive Assessment, Unified Parkinson's Disease Rating Scale 2 2 Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-02 ses-02 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-02/ses-02 Imaging 2 2 T1 Weighted, Flow Weighted freesurfer 7.3.2 Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-02 ses-02 Phenotypic 39 male Attention deficit hyperactivity disorder Montreal Cognitive Assessment, Unified Parkinson's Disease Rating Scale 2 2 Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-03 ses-01 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-03/ses-01 Imaging 2 2 T1 Weighted, Flow Weighted Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-03 ses-01 Phenotypic 22.1 Montreal Cognitive Assessment 2 2 Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-03 ses-02 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-03/ses-02 Imaging 2 2 T1 Weighted, Flow Weighted Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-03 ses-02 Phenotypic 23.2 Attention deficit hyperactivity disorder Montreal Cognitive Assessment, Unified Parkinson's Disease Rating Scale 2 2 Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-04 ses-01 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-04/ses-01 Imaging 2 2 T1 Weighted, Flow Weighted Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-04 ses-01 Phenotypic 21.1 female Unified Parkinson's Disease Rating Scale 2 2 Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-04 ses-02 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-04/ses-02 Imaging 2 2 T1 Weighted, Flow Weighted Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-04 ses-02 Phenotypic 22.3 female Montreal Cognitive Assessment, Unified Parkinson's Disease Rating Scale 2 2 Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-05 ses-01 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-05/ses-01 Imaging 2 2 T1 Weighted, Flow Weighted Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-05 ses-01 Phenotypic 42.5 male Attention deficit hyperactivity disorder Montreal Cognitive Assessment, Unified Parkinson's Disease Rating Scale 2 2 Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-05 ses-02 /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-05/ses-02 Imaging 2 2 T1 Weighted, Flow Weighted Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 +BIDS synthetic https://github.com/bids-standard/bids-examples 5 sub-05 ses-02 Phenotypic 43.2 male Attention deficit hyperactivity disorder Montreal Cognitive Assessment, Unified Parkinson's Disease Rating Scale 2 2 Flow Weighted, T1 Weighted fmriprep 23.1.3, freesurfer 7.3.2 \ No newline at end of file diff --git a/query-tool-results/dataset-level-results.tsv b/query-tool-results/dataset-level-results.tsv deleted file mode 100644 index 0d86958..0000000 --- a/query-tool-results/dataset-level-results.tsv +++ /dev/null @@ -1,2 +0,0 @@ -DatasetID DatasetName PortalURI NumMatchingSubjects AvailableImageModalities AvailablePipelines -http://neurobagel.org/vocab/838f54dd-bc3c-4469-8795-b5e280ae0f82 BIDS synthetic https://github.com/bids-standard/bids-examples 5 http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 \ No newline at end of file diff --git a/query-tool-results/participant-level-results-agg.tsv b/query-tool-results/participant-level-results-agg.tsv deleted file mode 100644 index d3f97ae..0000000 --- a/query-tool-results/participant-level-results-agg.tsv +++ /dev/null @@ -1,2 +0,0 @@ -DatasetID SubjectID SessionID SessionType Age Sex Diagnosis Assessment SessionFilePath NumPhenotypicSessions NumImagingSessions Modality CompletedPipelines -http://neurobagel.org/vocab/838f54dd-bc3c-4469-8795-b5e280ae0f82 protected protected protected protected protected protected protected protected protected protected protected protected \ No newline at end of file diff --git a/query-tool-results/participant-level-results.tsv b/query-tool-results/participant-level-results.tsv deleted file mode 100644 index 4088126..0000000 --- a/query-tool-results/participant-level-results.tsv +++ /dev/null @@ -1,31 +0,0 @@ -DatasetID SubjectID SessionID SessionType Age Sex Diagnosis Assessment SessionFilePath NumPhenotypicSessions NumImagingSessions Modality CompletedPipelines -http://neurobagel.org/vocab/838f54dd-bc3c-4469-8795-b5e280ae0f82 sub-01 ses-01 http://neurobagel.org/vocab/ImagingSession /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-01/ses-01 2 2 http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 -http://neurobagel.org/vocab/838f54dd-bc3c-4469-8795-b5e280ae0f82 sub-01 ses-01 http://neurobagel.org/vocab/PhenotypicSession 34.1 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