Australian-Imaging-Service pipelines issues

Australian-Imaging-Service / pipelines

Scripts to generate analysis pipelines that can be run in XNAT's container service

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[STORY] Analysis the .svs file using QuPath.

#328 anzhao opened 1 week ago
2
Upload XCP plugin to AIS GH repo and create GH Action to build JAR

#327 tclose opened 1 week ago
0
[STORY] Creating the PPT slides for oral presentation talk titled "XNAT + Neurodesk + JupyterHub: A Powerful Platform for Neuroimaging Analysis".

#326 anzhao opened 3 weeks ago
1
syntax updates to match pydra2app instead of arcana

#325 tclose closed 3 weeks ago
0
[STORY] Dan request to create script to remove spaces " " in folder names of any folder level of any folder structure.

#324 anzhao opened 1 month ago
0
[STORY] Create unittests for pipelines to test the AIS container service to be included in the AIS UAT

#323 tclose opened 1 month ago
0
[STORY] Work out why existing container service pipelines are not launching/running

#322 tclose opened 1 month ago
0
[STORY] Work out why staging server export directory is not accessible from scanner

#321 tclose closed 3 weeks ago
1
[STORY] Deploy the Jupyter Plugin for XNAT with PVC.

#320 anzhao opened 1 month ago
1
[STORY] Fix issue with dcm2bids-session launch

#319 tclose opened 1 month ago
0
[STORY] Implement proposed Pydra syntax

#318 tclose opened 2 months ago
0
[STORY] pydra2app ext command for installing new app to xnat

#317 tclose opened 2 months ago
0
[STORY] Write Jupyter notebook for workshop

#316 tclose opened 2 months ago
0
[STORY] Write bootstrapping pydra2app command to generate YAML

#315 tclose opened 2 months ago
0
[STORY] Split up Arcana into FrameTree, Pydra2App and core Arcana

#314 tclose closed 3 weeks ago
1
[STORY] JMX monitoring data needs to be collected for XNAT performance

#313 tclose opened 2 months ago
0
[STORY] Generation of human-readable reports from monitoring data from staging server

#312 tclose opened 2 months ago
0
[STORY] create the session label using patientID and study date with four underscore between them.

#311 anzhao closed 1 month ago
7
[STORY] Look into issue with large upload failures (>60GB)

#310 tclose opened 3 months ago
3
[STORY] Investigate S3 storage solutions

#309 tclose closed 1 month ago
2
Test ObjectiveFS to run the USyd AIS node directly on S3

#308 tclose closed 3 months ago
0
[STORY] Complete staging server startup script - Windows

#307 tclose opened 3 months ago
0
[STORY] Complete staging server startup script - Ubuntu

#306 tclose opened 3 months ago
0
[STORY] Monitoring of staging server processes

#305 tclose closed 2 months ago
0
[STORY] Upload Dan's sample data (63.7GB) to XNAT to test the de-identification script and remove the dose report, report pdf, request form “encapsulated” in a DICOM.

#304 anzhao closed 1 month ago
8
[STORY] 5TTgen investigation

#303 arkiev opened 4 months ago
2
[STORY] Fix AIS tech docs website

#302 tclose opened 4 months ago
0
[STORY] Manage security around NeuroDesk VMs

#301 tclose opened 4 months ago
1
[STORY] Set up institutional cache of NeuroDesk CVMFS server

#300 tclose opened 4 months ago
1
[STORY] Setup deidentification script for AILDR project

#299 tclose closed 4 months ago
3
[STORY] Add additional parcellation schemes to T1 processing pipeline

#298 arkiev closed 2 months ago
0
[FEATURE] Implement the Whole Slide Imaging (WSI) Datatype and new External Camera Protected (ECP) Datatype in XNAT.

#297 anzhao closed 3 weeks ago
8
[STORY] Test if it is possible to share two projects with the same Subject ID into a third within XNAT.

#296 anzhao closed 4 months ago
1
[EPIC] Apply Federated Learning into XNAT

#295 dwang-usyd opened 5 months ago
2
[STORY] Pydarfy different tools to do multimodal registration

#294 arkiev opened 5 months ago
1
[STORY] Document the setup of NeuroDesk on AIS (e.g. CVFMS)

#293 tclose closed 4 months ago
3
[STORY] Map out trajectory of pipelines

#292 arkiev closed 4 months ago
1
[STORY] Tournament of transformations

#291 arkiev closed 5 months ago
1
[STORY] XNATUploader bug fix, implementation and uploading testing.

#290 anzhao closed 4 months ago
3
[STORY] Loosen NFS permissions on TBP staging server dev VM

#289 tclose closed 6 months ago
2
[STORY] Test out neurodesk integration on EKS

#288 tclose closed 5 months ago
0
[STORY] Include JupyterHub image within AIS helm chart

#287 tclose closed 3 weeks ago
3
[STORY] Test for presence of manifest file in upload stage of xnat-ingest

#286 tclose opened 6 months ago
0
[STORY] Add support to logging via API to xnat-ingest commands

#285 tclose opened 6 months ago
0
[STORY] Configure USyd AIS k8s node to run "xnat-ingest" upload for TBP

#284 tclose closed 3 weeks ago
4
[STORY] Ensure that GHCR is accessible from staging server

#283 tclose closed 4 months ago
5
[BUG] Workflow checking for task outputs that have not been generated (FastSurfer task raises error at completion)

#282 arkiev closed 6 months ago
0
[BUG] fivettgen_hsvs_.py

#281 arkiev opened 6 months ago
0
[BUG] Filetype error at the end of `5TTgen_hsvs`

#280 arkiev opened 6 months ago
0
[STORY] Failure of TBP DICOM node (presumed after patch restart)

#279 tclose closed 6 months ago
1