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ANTsX / ANTsR

R interface to the ANTs biomedical image processing library
https://antsx.github.io/ANTsR
Apache License 2.0
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ENH: Add automated AIF mask generation. #292

Closed ntustison closed 4 years ago

ntustison commented 4 years ago

Previously, the function bloodPerfusionSVD required an arterial input function (AIF) mask image to generate the CBF, etc. images. This commit adds the ability to automatically generate a mask using this approach.

ntustison commented 4 years ago

Hey @stnava , this is the only commit I need before we can process the perfusion data. It's basically just a couple lines to process a single data set:

perfusionImage <- antsImageRead( perfusionFile )
voiMaskImage <- antsImageRead( brainMaskFile )

perfusion <- bloodPerfusionSVD( perfusionImage, voiMaskImage, thresholdSVD = 0.2, deltaTime = 1.0 )

antsImageWrite( perfusion$cbfImage, "cbfImage.nii.gz" )
antsImageWrite( perfusion$cbvImage, "cbvImage.nii.gz" )
antsImageWrite( perfusion$mttImage, "mttImage.nii.gz" )

but I've also added some visualization capabilities which I'll demonstrate in the example I'll send you after this gets merged.

muschellij2 commented 4 years ago

Weird - seeing failures on https://travis-ci.org/muschellij2/ANTsR/jobs/642453185#L10273 and https://travis-ci.org/ANTsX/ANTsR/jobs/641895019#L10206

ntustison commented 4 years ago

@muschellij2 Yeah, thanks for taking a look. I'm at a loss as to why those failures are occurring with this pull request.

stnava commented 4 years ago

sorry - I am stretched pretty thin til something like the 6th of February but might be able to look closer this upcoming weekend.

brian

On Mon, Jan 27, 2020 at 1:57 PM Nick Tustison notifications@github.com wrote:

@muschellij2 https://github.com/muschellij2 Yeah, thanks for taking a look. I'm at a loss as to why those failures are occurring with this pull request.

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ntustison commented 4 years ago

@stnava --- No urgency as I just pulled this branch to the local machine for processing the breacher data. Whenever you can is fine.