Skip to content

Commit

Permalink
Added to my own container to list of containers
Browse files Browse the repository at this point in the history
  • Loading branch information
jarrelscy authored and johnflavin committed Oct 15, 2024
1 parent 401ada7 commit b087335
Showing 1 changed file with 2 additions and 1 deletion.
3 changes: 2 additions & 1 deletion docs/list-of-containers-and-commands.md
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@ Contributions to this page are very welcome. These can be in the form of links t
| CONDR_METS lesion atlas | Misha / Flavin | | | Not published. 1. see [note on NIL Tools](#a-note-on-nil-tools). 2. This was built as a demo that relies on access to a non-public CNDA project. |
| niftyreg | Flavin / Marc Modat | Image not published | [nrgxnat/docker-images/niftyreg](https://github.com/NrgXnat/docker-images/tree/master/niftyreg) | Developed during container hackathon at UCL. I was unsure whether to publish this image or not, so I did not. |
| BIDS MRIQC | Flavin | N/A | [nrgxnat/docker-images/bids-mriqc](https://github.com/NrgXnat/docker-images/tree/master/bids-mriqc) | Not published as an image, only as a command. This fits the degin goal of the BIDS containers: use off-the-shelf BIDS docker images and write the command metadata to run them. |
| DICOM to DICOM JP2 compressed | jarrelscy | jarrelscy/dcm2jp2kdcm | [jarrelscy/dcm2jp2kdcm](https://github.com/jarrelscy/dcm2jp2kdcm) | Convert a session full of DICOM files to DICOM_COMPRESSED files which are jp2 encoded (Transfer syntax 1.2.840.10008.1.2.4.90). |

## Setup Containers

Expand Down Expand Up @@ -60,4 +61,4 @@ Many of the existing tools employed in the NRG lab—often as pipelines on CNDA
* The code should not be contained within a Docker image not controlled by NIL. This image would become the _de facto_ official release of the tools. If such an image were to exist, it should by all rights belong to the owner and creator of those tools: the NIL.
2. The tools often rely on the local availablity of atlas image files. Those altas images are available on the internal servers we have here, but are not generally available. If the atlases were included in a Docker image, its size would be many tens of gigabytes (typical sizes are tens to hundreds of megabytes). This would be prohibitive to install or develop against.

For this reason, any tool that is written using the NIL tools is not, in general, possible to containerize at this time. Exceptions are certainly possible; for instance, the lesion atlas image used only a few NIL tools, which could be copied directly into the Docker image itself. However, while this image can be created, is not distributable for reason 1. above.
For this reason, any tool that is written using the NIL tools is not, in general, possible to containerize at this time. Exceptions are certainly possible; for instance, the lesion atlas image used only a few NIL tools, which could be copied directly into the Docker image itself. However, while this image can be created, is not distributable for reason 1. above.

0 comments on commit b087335

Please sign in to comment.