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adds rules for composite warps from unfold and remove map to full grid #143

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merged 4 commits into from
Dec 26, 2021
Merged

adds rules for composite warps from unfold and remove map to full grid #143

merged 4 commits into from
Dec 26, 2021

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akhanf
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@akhanf akhanf commented Dec 22, 2021 •
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  • moves all compose warps rules to separate rules file
  • adds compose warp rules, and update to target rules
    TODO:
  • replace hacky orientation fix (this will take some effort to dig into -- if things work as is I suggest dealing with it later..)
  • remove map to full grid (no longer needed is map_to_full_grid needed? #128)
  • testing on real data

@akhanf
adds rules for composite warps from unfold
9573d09 
- moves all compose warps rules to separate rules file
- adds compose warp rules, and update to target rules
- TODO: replace hacky orientation fix
- TODO: testing on real data
@akhanf
removed maptofullgrid, updated naming accordingly
2321254 
- was able to remove the *_autotop/ folder directly, and instead write the
warp files using the usual bids naming

- the warps to transform surfaces are now named with mode=surface
instead of mode=image for the itk warps..

- moved all warp creation and composition to the warps.smk rule file
@akhanf
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akhanf commented Dec 22, 2021

@jordandekraker this should be ready for testing now..

@jordandekraker jordandekraker mentioned this pull request Dec 23, 2021
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akhanf and others added 2 commits December 23, 2021 08:14
@akhanf
fix a typo in create_warps outputs
b371ea2
@akhanf
fixes to get unfold2native warps working
42537ec 
- problem was with nifti reference space, not with orientation
- added a rule to create the ref space for warp files in native space
(similarly to what we already do for unfold space)
- moved ref vols to the seg_{modality} dir (were improperly sitting in the root
folder)
@akhanf akhanf marked this pull request as ready for review December 23, 2021 17:06
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akhanf commented Dec 23, 2021

it still had some errors, but now it should be working.. I've confirmed that the unfold2native warps are correct now too (problem wasn't with orientation but just using the right nifti reference space when creating them)..

@akhanf akhanf added the enhancement New feature or request label Dec 23, 2021
jordandekraker
jordandekraker approved these changes Dec 26, 2021
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Seems to be working on my end!

@jordandekraker jordandekraker mentioned this pull request Dec 26, 2021
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@akhanf akhanf merged commit 1d2924c into master Dec 26, 2021
@akhanf akhanf deleted the warps-rmfullgrid branch December 26, 2021 17:10
This was referenced Dec 26, 2021
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@akhanf @jordandekraker