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] Loosen NFS permissions on TBP staging server dev VM

#289 tclose closed 8 months ago
2
[STORY] Test out neurodesk integration on EKS

#288 tclose closed 7 months ago
0
[STORY] Include JupyterHub image within AIS helm chart

#287 tclose closed 2 months ago
3
[STORY] Test for presence of manifest file in upload stage of xnat-ingest

#286 tclose opened 8 months ago
0
[STORY] Add support to logging via API to xnat-ingest commands

#285 tclose opened 8 months ago
0
[STORY] Configure USyd AIS k8s node to run "xnat-ingest" upload for TBP

#284 tclose closed 2 months ago
4
[STORY] Ensure that GHCR is accessible from staging server

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

#282 arkiev closed 7 months ago
0
[BUG] fivettgen_hsvs_.py

#281 arkiev opened 8 months ago
0
[BUG] Filetype error at the end of `5TTgen_hsvs`

#280 arkiev opened 8 months ago
0
[STORY] Failure of TBP DICOM node (presumed after patch restart)

#279 tclose closed 8 months ago
1
[STORY] Configure XNAT-ingest workflow from TBP to AIS

#278 tclose closed 4 months ago
4
[STORY] Upgrade MSBase to 1.8.*

#277 tclose closed 5 months ago
4
[STORY] Finish off deployment of NIF AIS Node

#276 tclose opened 8 months ago
1
[STORY] GH action to build XNAT-ingest

#275 tclose closed 8 months ago
1
[STORY] Setup and test NeuroDesk integration with non-M1 chip

#274 tclose closed 8 months ago
2
[FEATURE] Total Body PET data ingestion

#273 tclose opened 8 months ago
1
[STORY] TBP staging server: automatically restore k8s after reboot

#272 tclose closed 4 months ago
2
[EPIC] Data Ingestion

#271 tclose opened 8 months ago
2
Added in prototype diffusion workflow

#270 tclose closed 9 months ago
0
[STORY] Investigate PET analysis pipeline that Malik sent

#269 tclose closed 3 months ago
1
[STORY] Finish porting of MRtrix3 Connectome BIDS app to Pydra

#268 tclose opened 9 months ago
0
[STORY] Check with NeuroDesk team that XNAT-launched containers are fully operational

#267 tclose closed 8 months ago
2
[STORY] Create cron/batch job to automatically update NeuroDesk

#266 tclose closed 7 months ago
2
[STORY] Create a video demo showing JupyterHub/NeuroDesk launch for presentation

#265 tclose closed 8 months ago
1
[STORY] Test launch of pipelines on k8s

#264 tclose closed 3 months ago
2
[FEATURE] Porting MRtrix3 Connectome to Pydra

#263 tclose opened 9 months ago
1
[STORY] NIF Reporting

#262 tclose closed 8 months ago
0
do test(s) to ensure input T1 will be adequately processed by FS

#261 arkiev opened 11 months ago
1
expand the catalogue to include parcellations that are not part of Free/FastSurfer (create separate story for this later)

#260 arkiev opened 11 months ago
0
tidy up working directory automatically (some sort of cleanup). Keep FS output dir.

#259 arkiev opened 11 months ago
0
run parcellation image generation in parallel

#258 arkiev opened 11 months ago
1
BIDS app review

#257 arkiev opened 11 months ago
0
[STORY] Merge T1 pipeline sections into a single script

#256 tclose closed 9 months ago
1
[STORY] Familiarising with AIS Helm chart

#255 tclose closed 11 months ago
1
[STORY] Write summary of AIS for Sydney Imaging Website

#254 tclose closed 7 months ago
0
[STORY] Implement a CI/CD pipeline to auto the deployment and updates of neurodesk and its associated applications.

#253 anzhao closed 7 months ago
0
[STORY] XNAT API bug that doesn't create an ldap account.

#252 anzhao closed 7 months ago
0
[STORY] Deploy T1-weighted pipeline as XNAT "app"

#251 tclose opened 1 year ago
0
[STORY] Adapting JupyterHub plugin so that the worker nodes can be launched on K8s

#250 tclose closed 9 months ago
19
[STORY] Install XNAT-JupyterHub plugin on AIS-XNAT instance and make it connects XNAT users to the JupyterHub server directly.

#249 tclose closed 7 months ago
0
[FEATURE] Integrate JupyterHub into AIS-XNAT.

#248 anzhao opened 1 year ago
2
[STORY] add catalogue of parcellation images to T1 processing pipeline

#247 arkiev closed 11 months ago
2
[FEATURE] Adapt JupyterHub plugin to be able to run NeuroDesk

#246 tclose opened 1 year ago
1
[FEATURE] ADEAPT XNAT datatypes

#245 tclose opened 1 year ago
1
expand FastSurfer task outputs to include images from /mri directory

#244 arkiev closed 1 year ago
1
zip `.mif` files

#243 arkiev closed 1 year ago
1
[FEATURE] TBP data transfer to AIS

#242 tclose opened 1 year ago
1
magic number error with `.mgz` file format

#241 arkiev closed 1 year ago
1
`labelconvert_.py` has repeating arguments in the `input_spec`

#240 arkiev opened 1 year ago
2

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