hippb500 workflow, output_spaces #38
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
workflow for pre-processed hippb500, and option for output_spaces
Check if all space-unfold files are being added as target rules
if cropT1w is in output_spaces, then use T1w (which will also genereate corobl as a dependency), but if not, then use corobl as the ref space
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
workflow for pre-processed hippb500, and option for output_spaces
Instead of using T1w to register to corobl, this workflow assumes hipp dwi (b500) is already in corobl space, and just performs a predefined crop to a predefined bounding box (shape used for training the CNN) for each hippocampus. This has been tested and working well with UAlberta dMRI protocol data. Note that the required pre-processed
_b500.nii.gzdata is not BIDS-compliant, but is the suffix used in snakedwi.Also adds an
output-spacescmdline param to specify what space output images are generated in (cropT1w is default, but corobl used for hippb500)To do:
adapt the workflow for corobl hippT2w perhaps?(maybe a different PR)