22 Aug 2018 |
| Chris Gorgolewskichanged room power levels. | 16:16:03 |
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| Oscar Esteban set the room topic to "https://docs.google.com/document/d/11gCzXOPUbYyuQx8fErtMO9tnOKC3kTWiL9axWkkILNE/edit#". | 17:07:04 |
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| Chris Markiewicz joined the room. | 17:08:16 |
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23 Aug 2018 |
Chris Gorgolewski | How did the first day go? | 01:09:41 |
Chris Markiewicz | Good. We completely deformatted the draft, but I'll clean it up tonight and I think we can narrow the discussion easily in the morning. | 01:45:30 |
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| Maarten Mennes changed their display name from Maarten to Maarten Mennes. | 14:51:50 |
Oscar Esteban | Welcome Mark! I'll try to update this room as soon as possible today | 16:33:31 |
Chris Gorgolewski | HI Mark! Glad you could join! | 16:34:07 |
Oscar Esteban | We are summarizing all the break-out groups at this moment | 16:34:30 |
Oscar Esteban | Okay, so some agreements:
- We agreed to strip the discussion about spaces off the common derivatives discussion (BEP003) to then report back when we have something concrete.
- We looked into the need of splitting the concepts of "space" (as defined by the scanner's or some other way of coordinate system) and "sampling" (a discretized space: images or surfaces)
- We started to work on how to specify spaces, as you can see in the working draft. Basically, they need to describe what is the image that was used as reference. This also diverted us to talk about how you specify a template space, and considered several options.
- We started to re-work the spaces tables from BEP003
- We also saw necessary to define a "universal" transform specification that will be implemented in a software tool which purpose is 1) understanding (read/write) major formats of linear/nonlinear transforms; and 2) apply transforms to images and surfaces/point sets. The seed of this WIP is here: https://github.com/nipy/nibabel/pull/656
- We roughly agreed that the easiest way of writing this "universal" transforms on files is HDF5 (although, this would not follow ITK's current h5 format).
- We started with how these files will be named. They will have a mandatory json file that should specify what method was used to calculate the corresponding transform.
- We tried to tie together the many concepts software tools use to denote the same entities: "reference", "fixed" image and "moving", "target", "input" image. We initially agreed that a possible option is "from" and "to".
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24 Aug 2018 |
| Oscar Esteban invited edickie. | 06:35:56 |
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31 Aug 2018 |
Chris Markiewicz | To keep momentum up, I think we want to move relatively quickly on getting a version 1 of the .x5 format going. Is there a separate document from BEP 14 that has proposals (I'm seeing a few desiderata, but not much else, there)? Or mailing list attempts to rope in people who are very familiar with the details of existing warp formats? | 14:47:40 |
Chris Markiewicz | I think we could iterate through a few versions pretty quickly, so even if v1 only includes, e.g. ANTs and FSL warp transforms, we could then move on to v2 to add FreeSurfer spherical warps, or whatever. | 14:49:09 |
Chris Gorgolewski | I think it might be wise to get a prototype of the format with a good description, before going public. | 14:49:26 |