BEP014: Transformations

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https://docs.google.com/document/d/11gCzXOPUbYyuQx8fErtMO9tnOKC3kTWiL9axWkkILNE/edit#1 Servers

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22 Aug 2018
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23 Aug 2018
01:09:41@filo:matrix.orgChris GorgolewskiHow did the first day go?
01:45:30@markiewicz:matrix.orgChris 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.
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16:33:31@oesteban:matrix.orgOscar EstebanWelcome Mark! I'll try to update this room as soon as possible today
16:34:07@filo:matrix.orgChris GorgolewskiHI Mark! Glad you could join!
16:34:30@oesteban:matrix.orgOscar EstebanWe are summarizing all the break-out groups at this moment
18:17:51@oesteban:matrix.orgOscar 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".
24 Aug 2018
06:35:56@oesteban:matrix.orgOscar Esteban invited @edickie:matrix.orgedickie.
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31 Aug 2018
14:47:40@markiewicz:matrix.orgChris MarkiewiczTo 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?
14:49:09@markiewicz:matrix.orgChris MarkiewiczI 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.
14:49:26@filo:matrix.orgChris GorgolewskiI think it might be wise to get a prototype of the format with a good description, before going public.
14:50:14@markiewicz:matrix.orgChris MarkiewiczFair.
14:51:52@markiewicz:matrix.orgChris Markiewicz@oesteban @satra
14:52:42@markiewicz:matrix.orgChris Markiewicz Oscar Esteban satra Is the section in BEP 14 the current draft, or is there a separate doc?
9 Sep 2018
19:15:08@satra:matrix.orgsatra Oscar Esteban:
19:15:24@satra:matrix.orgsatra Oscar Esteban: there is no separate doc.

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