graddev integration #43
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and perform ci to trigger dockerhub push to hippunfold
Updating to rebuild container using latest version
was timing out
- still a work in progress, but should be a "mostly" working version now! - relies on https://github.com/akhanf/snakebids for bids grabbing and CLI (which is still also under construction) - includes https://github.com/jordandekraker/Hippocampal_AutoTop as a submodule for the core unfolding code - pre-processing for T1w, T2w, and dwi (currently dwi processing limited to data that can be run through topup, e.g. multiple phase encode repeats) - workflow is not yet packaged into a single container yet -- will work on that - please add more feature requests as github issues!
* added input seg, moved all anat preproc to same folder * updates for limiting workflow to the specified modalities * removed snakebids fixed version * added arg for derivatives, and fixed grabbing segs * change manual seg interp to nearest neighbor Co-authored-by: Roy Haast <[email protected]>
was missing a conversion to itk warp, and had unfold vs native swapped
Patch itkwarps, numpy version
still need to test this out, and create a snakemake rule to generate the graddev file based on the coordinates using either code from these classes, or using the existing api
rebase to master
- fixes orientation bug in WarpITK_unfold2native.nii - adds rules for composing unfold to cropT1w space transforms - NOTE: had to use antsApplyTransforms for this, since ComposeMultiTransform was buggy -- consider replacing ComposeMultiTransform in the composition the other way around too.
Missed a comma
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warp composition is incorporated in #143 |
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This PR is for creating the graddev file from the coords to allow us to do dwi fitting in unfolded space.
@Bradley-Karat let's use this branch to implement the new functionality. We can walk through this together as it is the best way to learn..
So far I have put the files you gathered into the
hippunfold/tmp_from_uzairfolder..First step for you would be to create a local virtualenv to develop in, e.g. see: https://hippunfold.readthedocs.io/en/latest/getting_started/installation.html#setting-up-a-dev-environment-on-graham
Then try getting the
example.pycode working. We may need to add some packages to the requirements for that too..Then we can figure out what functionality we want to add into the workflow and how..